File: bed2region

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libvcflib 1.0.12%2Bdfsg-1
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#!/usr/bin/env perl
# convert VCF CHROM column in VCF file to region

# Example
#
# #CHROM:POS-ID   REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001 NA00002 NA00003 ...
# 20:1110696-rs6040355    A       G,T     67      PASS    NS=2;DP=10;AF=0.333,0.667;AA=T;DB ...

while (<STDIN>) {
    $_ =~ /^(.+?)\s(.+?)\s(.+)\s*/;
    $chrom = $1;
    $pos = $2;
    $end = $3;
    print $chrom . ":" . $pos . "-" . $end . "\n";
}