How to convert indel vcf files to SNPT input files

How to convert indel vcf files into SNPT input files, this article introduces the corresponding analysis and solutions in detail, hoping to help more partners who want to solve this problem to find a more simple and easy way.

How to convert indel vcf files into input files of SNPT software.

SNP fingerprint software SNPT, here record how to convert the indel vcf file into the input file of the SNPT software.

The command is as follows:

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

The vcf_SNPT.indel.pl script is as follows:

#! / 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, "infile" = >\ $out) or & USAGE;&USAGE unless ($infile and $out); sub USAGE {# my $usage=