#!/bin/bash -Ceuo pipefail
set -euo pipefail
nipt_emit_alpha_features.py \
    --vcf HG03540_x_HG03579_FF_10.vcf \
    --bam HG03540_x_HG03579_FF_10.mix.bam \
    --ref Homo_sapiens_assembly38.fasta \
    --out-tsv HG03540_x_HG03579_FF_10.features.tsv \
    --out-vcf HG03540_x_HG03579_FF_10.augmented.vcf \
    --target-tsv HG03540_x_HG03579_FF_10.targets.tsv \
    --indels-only \
    --ff 0.1 \
    --alphas 0.012,0.05,0.10 \
    --window-pad 250 \
    --min-mapq 20 \
    --progress 100 2>&1 | tee HG03540_x_HG03579_FF_10.log