#!/bin/bash -euo pipefail
nipt_call_variants.py \
    --bam 10pct-FF-HG00733.md.bam \
    --ref Homo_sapiens_assembly38.fasta \
    --output 10pct-FF-HG00733_shard_0048.vcf \
    --sample-name 10pct-FF-HG00733 \
    --ff 0.1 \
    --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_0048.bed \
    --parallel --n-workers 16 \
    --no-qc \
    --extract-posteriors \
     \
     \
     \