#!/bin/bash -Ceuo pipefail
python /usr/local/bin/call_cnv.py \
    --tumor-parquet 1029_11H-T1-TDNA-1_B23KFCWLT4_1_normalized.parquet \
    --normal-parquet 1029_11H-N1-BDNA-1_B23KGCJLT4_1_normalized.parquet \
    --pairs test_pairs.tsv \
    --specimen 1029_11H \
    --output 1029_11H_segments.tsv \
    --tumor-alleles 1029_11H-T1-TDNA-1_B23KFCWLT4_1_alleles.tsv.gz \
    --normal-alleles 1029_11H-N1-BDNA-1_B23KGCJLT4_1_alleles.tsv.gz \
    --probe-agg-output 1029_11H_probe_agg.tsv.gz \
    --plots-dir plots \
    --metrics-output 1029_11H_metrics.tsv \
    --workers 4 \
    --genes-bed altera_genes_hg38.bed \
    --genome-annotations Homo_sapiens.GRCh38.110.gtf.gz \
    --gene-output 1029_11H_gene_cnv.tsv \
    --vcf-output 1029_11H_somatic.vcf \
    --fit-method clonal-decomp --mode ascn