.command.sh - Workdir - NIPT_CALLING:NIPT_CALL_VARIANTS (5pct-FF-HG00733_shard_0025)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/5f02fb2dc2f816d38f3c2478a54cee/.command.sh
Size: 567 bytes
Task: NIPT_CALLING:NIPT_CALL_VARIANTS (5pct-FF-HG00733_shard_0025)
Attempt

Content

#!/bin/bash -euo pipefail
nipt_call_variants.py \
    --bam 5pct-FF-HG00733.md.bam \
    --ref Homo_sapiens_assembly38.fasta \
    --output 5pct-FF-HG00733_shard_0025.vcf \
    --sample-name 5pct-FF-HG00733 \
    --ff 0.05 \
    --min-depth 150 \
    --min-mapq 20 \
    --min-alt-count 1 \
    --min-alt-frac 0.01 \
    --min-gq 5 \
    --max-strand-bias 0.9 \
    --default-af 0.5 \
    --graph-score-min -6.5 \
    --gnomad gnomad_af.tsv.gz \
    --bed shard_0025.bed \
    --parallel --n-workers 16 \
    --no-qc \
    --extract-posteriors \
     \
     \
     \