.command.sh - Workdir - EMIT_ALPHA_FEATURES (HG00621_x_HG00673_FF_5)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/476a06801d17b6e6a8c39ff239c268/.command.sh
Size: 525 bytes
Task: EMIT_ALPHA_FEATURES (HG00621_x_HG00673_FF_5)
Attempt

Content

#!/bin/bash -Ceuo pipefail
set -euo pipefail
nipt_emit_alpha_features.py \
    --vcf HG00621_x_HG00673_FF_5.vcf \
    --bam HG00621_x_HG00673_FF_5.mix.bam \
    --ref Homo_sapiens_assembly38.fasta \
    --out-tsv HG00621_x_HG00673_FF_5.features.tsv \
    --out-vcf HG00621_x_HG00673_FF_5.augmented.vcf \
    --target-tsv HG00621_x_HG00673_FF_5.targets.tsv \
    --indels-only \
    --ff 0.05 \
    --alphas 0.012,0.05,0.10 \
    --window-pad 250 \
    --min-mapq 20 \
    --progress 100 2>&1 | tee HG00621_x_HG00673_FF_5.log