1#!/usr/bin/env perl 2# 3 4while (<STDIN>) { 5 if ($_ =~ /^#/) { 6 print; 7 } else { 8 $_ =~ /^(.+?)\t(.+?)\t(.+?)\t(.+?)\t(.+?)\t/; 9 $chrom = $1; 10 $pos = $2; 11 $tag = $3; 12 $ref = $4; 13 $alts = $5; 14 $hasnonsnp = 0; 15 $biallelic = 1; 16 if ($alts =~ /,/) { 17 $biallelic = 0; 18 } 19 @alts = split(/,/, $alts); 20 foreach $alt (@alts) { 21 if (!(length($alt)==1 && length($alt) == length($ref))) { 22 $hasnonsnp = 1; 23 } 24 } 25 if ($hasnonsnp || !$biallelic) { 26 print; 27 } 28 } 29} 30