.command.sh - Workdir - NIPT_CALLING:NIPT_CALL_VARIANTS (fetal_AF_5_shard_0018)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/eba66305742dae3814f78cd8e8debd/.command.sh
Size: 565 bytes
Task: NIPT_CALLING:NIPT_CALL_VARIANTS (fetal_AF_5_shard_0018)
Attempt

Content

#!/bin/bash -euo pipefail
nipt_call_variants.py \
    --bam fetal_AF_5.dedup.bam \
    --ref Homo_sapiens_assembly38.fasta \
    --output fetal_AF_5_shard_0018.vcf \
    --sample-name fetal_AF_5 \
    --ff 0.05 \
    --min-depth 300 \
    --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 -5.5 \
    --gnomad gnomad_af.tsv.gz \
    --bed shard_0018.bed \
    --parallel --n-workers 32 \
    --no-qc \
    --extract-posteriors \
     \
    --assembly \
     \