#!/bin/bash

INPUT_FILE="morex_v2_arf_location.txt"
VCF_IN="merged_all.vcf.gz"

while IFS=$'\t' read -r chrom start end name; do
  region="${chrom}:${start}-${end}"
  out_vcf="${name}_2.vcf.gz"

  echo "Extracting $region to $out_vcf"
  bcftools view -r "$region" "$VCF_IN" -Oz -o "$out_vcf"
done < "$INPUT_FILE"