#!/bin/bash -euo pipefail
nipt_call_variants.py \
--bam 2026-0071_HG00733_HG00732_pure_fetal.ds.bam \
--ref Homo_sapiens_assembly38.fasta \
--output 2026-0071_HG00733_HG00732_pure_fetal_shard_0039.vcf \
--sample-name 2026-0071_HG00733_HG00732_pure_fetal \
--ff 1.0 \
--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_0039.bed \
--parallel --n-workers 16 \
--no-qc \
--extract-posteriors \
\
\
\