.command.sh - Workdir - EMIT_ALPHA_FEATURES (HG01109_x_HG01175_FF_5)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/700cfd56144c8ac6213c7786eeabdd/.command.sh
Size: 525 bytes
Task: EMIT_ALPHA_FEATURES (HG01109_x_HG01175_FF_5)
Attempt

Content

#!/bin/bash -Ceuo pipefail
set -euo pipefail
nipt_emit_alpha_features.py \
    --vcf HG01109_x_HG01175_FF_5.vcf \
    --bam HG01109_x_HG01175_FF_5.mix.bam \
    --ref Homo_sapiens_assembly38.fasta \
    --out-tsv HG01109_x_HG01175_FF_5.features.tsv \
    --out-vcf HG01109_x_HG01175_FF_5.augmented.vcf \
    --target-tsv HG01109_x_HG01175_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 HG01109_x_HG01175_FF_5.log