indel vcf文件如何转化为SNPT输入文件

indel vcf文件如何转化为SNPT输入文件，针对这个问题，这篇文章详细介绍了相对应的分析和解答，希望可以帮助更多想解决这个问题的小伙伴找到更简单易行的方法。

如何将indel vcf文件转换为SNPT软件的输入文件。

SNP指纹图谱软件SNPT ，这里记录一下如何将indel vcf文件转换为SNPT软件的输入文件。

命令如下：

perl /share/work/wangq/script/vcf/vcf_SNPT.indel.pl -vcf clean.vcf -o SNPT.input.txt

vcf_SNPT.indel.pl脚本如下：

#!/share/nas2/genome/bin/perl -w#use strict;#use warnings;use Getopt::Long;use List::Util qw(shuffle);use Data::Dumper;use FindBin qw($Bin $Script);use File::Basename qw(basename dirname);use Cwd qw(abs_path);my $version="1.0.0";my $BEGIN_TIME=time();my @Original_ARGV=@ARGV;# ==============================================================# Get Options# ==============================================================my ($infile, $indexOut, $p);GetOptions(                                "help|?" =>\&USAGE,                                "vcf:s"=>\$infile,                                "o:s"=>\$out                                ) or &USAGE;&USAGE unless ($infile and $out);sub USAGE {#        my $usage=<<"USAGE";Program: $0Version: $version==================================================================================================Discription:        This script is used to calculate thresold for BSA using SNP-INDEX method==================================================================================================Usage:  Options:  -vcf             required        vcf list file  -o             required        output fileUSAGE        print $usage;        exit;}#===============================================================# Default optional value#===============================================================open (IN, "<$infile") || die "$infile: $!\n";open (OUT, ">$out") || die "$out: $!\n";my @sample;my %snp;my @indel;while(){        chomp;        next if(/^##/);        my ($chr,$pos,$id,$ref,$alt,$qual,$filter,$info,$format,@line) = split(/\t/,$_);        if(/^#/){                @sample = @line;                next;        }        my @array = $_=~/\t([\.0123][\/\|][\.0123])/g;        if(@array != @sample ){                print "SNP $chr,$pos length not eq.\n";                next;        }        my $chr_indel= "$chr-$pos";        push(@indel,$chr_indel);        for(my$i =0; $i<@line ;$i++){                my $str;                if($array[$i] eq "0/0" || $array[$i] eq "0|0" ){                        $str = "A";                }elsif($array[$i] eq "0/1" || $array[$i] eq "0|1" ){                        $str = "C";                }elsif($array[$i] eq "1/1" || $array[$i] eq "1|1" ){                        $str = "G";                }else{                        $str = "T";                }                $snp{$chr_indel}{$sample[$i]} = $str;        }}close(IN);print OUT join("\t","Strain",@indel)."\t";for($i=0; $i < @sample ; $i++){        print OUT "$sample[$i]";        for($j=0; $j < @indel ; $j++){                #print "1";                print OUT "\t$snp{$indel[$j]}{$sample[$i]}";        }        print OUT "\n";}close(OUT);

关于indel vcf文件如何转化为SNPT输入文件问题的解答就分享到这里了，希望以上内容可以对大家有一定的帮助，如果你还有很多疑惑没有解开，可以关注行业资讯频道了解更多相关知识。