File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/e612edcf59fd4a1a01fdbcf1d08369/.command.sh
Size
614 bytes
Attempt
#!/bin/bash -euo pipefail
nipt_call_variants.py \
    --bam 2026-0078_HG00732_pure_maternal.ds.bam \
    --ref Homo_sapiens_assembly38.fasta \
    --output 2026-0078_HG00732_pure_maternal_shard_0038.vcf \
    --sample-name 2026-0078_HG00732_pure_maternal \
    --ff 0.0 \
    --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 -6.5 \
    --gnomad gnomad_af.tsv.gz \
    --bed shard_0038.bed \
    --parallel --n-workers 16 \
    --no-qc \
    --extract-posteriors \
     \
     \
     \