Alaina Hardie trianglegrrl
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| name: sra_download | |
| description: use Google Pipeline API to download an SRA run, reformat it as unaligned BAM, and upload it to Google Cloud Storage. Run it like this: gcloud alpha genomics pipelines run --inputs SAMPLE=XXXXX --inputs RUN=XXXXX --outputs OUTPUT_FILE=gs://XXXXX --pipeline-file=sra_download.yaml | |
| resources: | |
| #increase boot disk from 10GB to 50GB to accomodate intermediate files | |
| bootDiskSizeGb: 50 | |
| #specify multiple zones so this pipeline will run in parallel | |
| zones: | |
| - us-west1-a | |
| - us-west1-b | |
| - us-east1-b |
ShujiaHuang
/ gatk_bundle_and_WGS_test_data.sh
Last active
October 22, 2024 17:22
Common datasets for GATK
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| #Known datasets: GATK bundle for human b37 reference | |
| # | |
| wget -c ftp://[email protected]/bundle/b37/dbsnp_138.b37.vcf.gz.md5 | |
| wget -c ftp://[email protected]/bundle/b37/dbsnp_138.b37.vcf.gz | |
| wget -c ftp://[email protected]/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz | |
| wget -c ftp://[email protected]/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz.md5 | |
| wget -c ftp://[email protected]/bundle/b37/1000G_phase1.indels.b37.vcf.gz | |
| wget -c ftp://[email protected]/bundle/b37/1000G_phase1.indels.b37.vcf.gz.md5 | |
| wget -c ftp://[email protected]/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz | |
| wget -c ftp://[email protected]/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz.md5 |