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December 22, 2014 10:54
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| details: | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 10152-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/10152-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/10152-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [10152-tumor2_vs_normal, 10152-tumor_vs_normal, 10152-tumor3_old_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 10152-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/10152-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/10152-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 10152-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 10152-tumor2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/10152-tumor2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/10152-tumor2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 10152-tumor2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 10152-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/10152-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/10152-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 10152-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20144-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20144-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20144-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20144-tumor2_2_vs_normal, 20144-tumor2_1_vs_normal, 20144-tumor_vs_normal, 20144-tumor3_old_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20144-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20144-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20144-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20144-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20144-tumor2_1 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20144-tumor2_1_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20144-tumor2_1_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20144-tumor2_1_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20144-tumor2_2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20144-tumor2_2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20144-tumor2_2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20144-tumor2_2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20144-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20144-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20144-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20144-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20357-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20357-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20357-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20357-tumor_vs_normal, 20357-tumor3_old_vs_normal, 20357-tumor2_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20357-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20357-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20357-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20357-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20357-tumor2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20357-tumor2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20357-tumor2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20357-tumor2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20357-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20357-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20357-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20357-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20367-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20367-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20367-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20367-tumor_1_vs_normal, 20367-tumor_vs_normal, 20367-tumor3_old_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20367-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20367-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20367-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20367-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20367-tumor_1 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20367-tumor_1_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20367-tumor_1_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20367-tumor_1_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20367-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20367-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20367-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20367-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20418-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20418-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20418-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20418-tumor_vs_normal, 20418-tumor3_old_vs_normal, 20418-tumor2_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20418-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20418-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20418-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20418-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20418-tumor2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20418-tumor2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20418-tumor2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20418-tumor2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20418-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20418-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20418-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20418-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20614-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20614-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20614-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20614-tumor_vs_normal, 20614-tumor3_old_vs_normal, 20614-tumor2_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20614-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20614-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20614-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20614-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20614-tumor2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20614-tumor2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20614-tumor2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20614-tumor2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20614-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20614-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20614-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20614-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20654-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20654-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20654-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20654-tumor_1_vs_normal, 20654-tumor_vs_normal, 20654-tumor3_old_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20654-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20654-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20654-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20654-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20654-tumor_1 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20654-tumor_1_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20654-tumor_1_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20654-tumor_1_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20654-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20654-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20654-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20654-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20663-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20663-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20663-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20663-tumor_vs_normal, 20663-tumor3_old_vs_normal, 20663-tumor2_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20663-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20663-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20663-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20663-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20663-tumor2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20663-tumor2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20663-tumor2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20663-tumor2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20663-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20663-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20663-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20663-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20681-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20681-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20681-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20681-tumor_vs_normal, 20681-tumor3_old_vs_normal, 20681-tumor2_vs_normal, 20681-tumor3_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20681-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20681-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20681-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20681-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20681-tumor3 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20681-tumor3_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20681-tumor3_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20681-tumor3_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20681-tumor2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20681-tumor2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20681-tumor2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20681-tumor2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20681-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20681-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20681-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20681-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20683-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20683-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20683-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20683-tumor_1_vs_normal, 20683-tumor_vs_normal, 20683-tumor3_old_vs_normal, 20683-tumor3_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20683-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20683-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20683-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20683-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20683-tumor3 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20683-tumor3_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20683-tumor3_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20683-tumor3_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20683-tumor_1 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20683-tumor_1_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20683-tumor_1_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20683-tumor_1_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20683-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20683-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20683-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20683-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20724-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20724-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20724-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20724-tumor2_vs_normal, 20724-tumor_vs_normal, 20724-tumor3_old_vs_normal, 20724-tumor3_5_vs_normal, 20724-tumor3_4_vs_normal, 20724-tumor3_3_vs_normal, 20724-tumor3_2_vs_normal, 20724-tumor3_1_vs_normal, 20724-met-tumor_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20724-tumor3_1 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20724-tumor3_1_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20724-tumor3_1_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20724-tumor3_1_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20724-tumor3_2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20724-tumor3_2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20724-tumor3_2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20724-tumor3_2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20724-tumor3_3 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20724-tumor3_3_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20724-tumor3_3_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20724-tumor3_3_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20724-tumor3_4 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20724-tumor3_4_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20724-tumor3_4_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20724-tumor3_4_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20724-tumor3_5 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20724-tumor3_5_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20724-tumor3_5_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20724-tumor3_5_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20724-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20724-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20724-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20724-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20724-met-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20724-met-tumor_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20724-met-tumor_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20724-met-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20724-tumor2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20724-tumor2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20724-tumor2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20724-tumor2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20724-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20724-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20724-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20724-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20738-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20738-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20738-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20738-tumor_vs_normal, 20738-tumor3_old_vs_normal, 20738-tumor2_2_vs_normal, 20738-tumor2_1_vs_normal, 20738-tumor3_1_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20738-tumor3_1 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20738-tumor3_1_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20738-tumor3_1_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20738-tumor3_1_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20738-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20738-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20738-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20738-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20738-tumor2_1 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20738-tumor2_1_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20738-tumor2_1_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20738-tumor2_1_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20738-tumor2_2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20738-tumor2_2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20738-tumor2_2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20738-tumor2_2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20738-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20738-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20738-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20738-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20788-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20788-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20788-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20788-tumor2_vs_normal, 20788-tumor_vs_normal, 20788-tumor3_old_vs_normal, 20788-tumor3_2_vs_normal, 20788-tumor3_1_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20788-tumor3_1 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20788-tumor3_1_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20788-tumor3_1_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20788-tumor3_1_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20788-tumor3_2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20788-tumor3_2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20788-tumor3_2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20788-tumor3_2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20788-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20788-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20788-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20788-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20788-tumor2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20788-tumor2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20788-tumor2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20788-tumor2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20788-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20788-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20788-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20788-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20800-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20800-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20800-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20800-tumor_vs_normal, 20800-tumor3_old_vs_normal, 20800-tumor2_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20800-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20800-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20800-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20800-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20800-tumor2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20800-tumor2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20800-tumor2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20800-tumor2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20800-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20800-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20800-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20800-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20821-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20821-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20821-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20821-tumor_vs_normal, 20821-tumor3_old_vs_normal, 20821-tumor3_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20821-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20821-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20821-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20821-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20821-tumor3 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20821-tumor3_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20821-tumor3_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20821-tumor3_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20821-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20821-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20821-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20821-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20924-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20924-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20924-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20924-tumor_vs_normal, 20924-tumor3_old_vs_normal, 20924-tumor3_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20924-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20924-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20924-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20924-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20924-tumor3 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20924-tumor3_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20924-tumor3_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20924-tumor3_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20924-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20924-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20924-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20924-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20935-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20935-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20935-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20935-tumor_vs_normal, 20935-tumor3_old_vs_normal, 20935-tumor2_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20935-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20935-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20935-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20935-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20935-tumor2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20935-tumor2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20935-tumor2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20935-tumor2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20935-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20935-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20935-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20935-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20995-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20995-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20995-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [20995-tumor_vs_normal, 20995-tumor3_old_vs_normal, 20995-tumor2_4_vs_normal, 20995-tumor2_3_vs_normal, 20995-tumor2_2_vs_normal, 20995-tumor2_1_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20995-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20995-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20995-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20995-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20995-tumor2_1 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20995-tumor2_1_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20995-tumor2_1_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20995-tumor2_1_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20995-tumor2_2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20995-tumor2_2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20995-tumor2_2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20995-tumor2_2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20995-tumor2_3 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20995-tumor2_3_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20995-tumor2_3_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20995-tumor2_3_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20995-tumor2_4 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20995-tumor2_4_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20995-tumor2_4_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20995-tumor2_4_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 20995-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/20995-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/20995-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 20995-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21019-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21019-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21019-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [21019-tumor2_vs_normal, 21019-tumor_vs_normal, 21019-tumor3_old_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21019-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21019-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21019-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 21019-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21019-tumor2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21019-tumor2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21019-tumor2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 21019-tumor2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21019-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21019-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21019-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 21019-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21110-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21110-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21110-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [21110-tumor_vs_normal, 21110-tumor3_old_vs_normal, 21110-tumor2_2_vs_normal, 21110-tumor2_1_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21110-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21110-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21110-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 21110-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21110-tumor2_1 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21110-tumor2_1_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21110-tumor2_1_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 21110-tumor2_1_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21110-tumor2_2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21110-tumor2_2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21110-tumor2_2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 21110-tumor2_2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21110-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21110-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21110-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 21110-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21184-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21184-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21184-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [21184-tumor_vs_normal, 21184-tumor3_old_vs_normal, 21184-tumor2_vs_normal, 21184-tumor2-ovaio-control_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21184-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21184-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21184-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 21184-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21184-tumor2-ovaio-control | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21184-tumor2-ovaio-control_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21184-tumor2-ovaio-control_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 21184-tumor2-ovaio-control_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21184-tumor2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21184-tumor2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21184-tumor2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 21184-tumor2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21184-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21184-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21184-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 21184-tumor_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21296-normal | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21296-normal_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21296-normal_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: [21296-tumor_vs_normal, 21296-tumor3_old_vs_normal, 21296-tumor2_vs_normal] | |
| phenotype: normal | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21296-tumor3_0 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21296-tumor3_old_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21296-tumor3_old_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 21296-tumor3_old_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21296-tumor2 | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21296-tumor2_R1_001.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21296-tumor2_R2_001.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 21296-tumor2_vs_normal | |
| phenotype: tumor | |
| - algorithm: | |
| aligner: bwa | |
| archive: cram | |
| clinical_reporting: true | |
| coverage: my_regions | |
| coverage_depth: high | |
| coverage_interval: regional | |
| effects: vep | |
| indelcaller: scalpel | |
| mark_duplicates: false | |
| min_allele_fraction: 1 | |
| mixup_check: qsignature | |
| platform: illumina | |
| quality_format: Standard | |
| realign: false | |
| recalibrate: false | |
| remove_lcr: true | |
| trim_reads: false | |
| variant_regions: my_regions | |
| variantcaller: | |
| - mutect | |
| - freebayes | |
| - vardict | |
| write_summary: true | |
| ensemble: | |
| numpass: 2 | |
| analysis: variant2 | |
| description: 21296-tumor | |
| files: | |
| - /mnt/data/projects/raw_data/panel/21296-tumor_R1.fastq.gz | |
| - /mnt/data/projects/raw_data/panel/21296-tumor_R2.fastq.gz | |
| genome_build: hg19 | |
| metadata: | |
| batch: 21296-tumor_vs_normal | |
| phenotype: tumor | |
| fc_date: '2014-12-17' | |
| fc_name: Current_run | |
| globals: | |
| my_regions: /mnt/data/projects/regions/regions.sorted.bed | |
| upload: | |
| dir: ../final/ |
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