#!/bin/bash -Ceuo pipefail
set -euo pipefail
dedupe \
    --input_bam_path 'one.markdup.bam' \
    --output_bam_file 'one.deduped.bam' \
    --selector_path 'small_padded.bed' \
    --threads 4 \
    --stats-file 'one.deduped.stats.csv' \
    --max_read_snvs 0.05 \
    --min_qual_score 30 \
    --min_frag_len 60 \
    --max_frag_len 800 \
    --min_var_ratio 0.5 \
    --min_var_reads 1 \
    --max_low_qual 0.1 \
    --variant_threshold 5
samtools index -@ 4 one.deduped.bam one.deduped.bam.bai