Alaina Hardie trianglegrrl
ShujiaHuang
/ gatk_bundle_and_WGS_test_data.sh
Last active
October 22, 2024 17:22
Common datasets for GATK
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |