代码如下:
#!/usr/bin/perl -w use strict; die "perl $0 <vcf> <genome>" if(@ARGV == 0); #Author:yueyao@genomics.cn my $vcf=shift; my $genome=shift; my%hash; my $id; open GENOME,$genome or die $!; while(<GENOME>){ chomp; if(/^>/){ $id=$_; $id=~s/>//; $id=~s/ //g; }else{ $hash{$id} .= $_; } } close GENOME; my@temp; my$pos; my$start; my$end; my$len; my$seq; my$fetchseq; my($refindelseq,$altindelseq,$upseq,$downseq,$downstart,$refindellen,$upend,$upstart); open VCF,$vcf or die $!; while(<VCF>){ chomp; next if(/^Chr/); @temp=split/\t/; if(exists $hash{$temp[0]}){ $seq=$hash{$temp[0]}; $pos=$temp[1]; $refindelseq=$t