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Commands used for running JHU samples on DeepVariant:
All files and sample sheets are first staged in S3 buckets linked to NFTower. then the following command are used to launch the processing pipeline.
Params:
| Code Block |
|---|
input: s3://jhu-biobank-nf-project-tower-bucket/jobs/02-sage-sarek-2.7.1-deepvariant/inputs/sample-sheet.tsv outdir: s3://jhu-biobank-nf-project-tower-bucket/jobs/02-sage-sarek-2.7.1-deepvariant/outputs/ genome: GRCh38 igenomes_base: s3://sage-igenomes/igenomes model_type: WES tools: "deepvariant" |
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