prod_reproduction/202307-FMBY2/script/trim_manta_tandem.pl

#!/usr/bin/perl

use strict;
use warnings;

my $genome=shift;

while(<STDIN>){
    if(/^#/){
        print ;
        next;
    }
    my ($chr,$pos,$id,$ref,$alt,$qual, $filter,$other)=split /\t/, $_, 8;
    next unless $filter eq 'PASS';
    next if $other=~/IMPRECISE/;
    if($alt eq '<DUP:TANDEM>' or $alt eq '<DEL>'){
        my ($end)=$other=~/END=(\d+)/;
        my $new_end;
        if ($end - $pos > 10000){
            $new_end+=$pos+10000
        }elsif($end < $pos){
            next
        }else{
            $new_end=$end
        }
        my $seq=`samtools faidx $genome $chr:$pos-$new_end |awk 'NR>1'`;
        $seq=~s/\s//g;
        print join("\t",$chr,$pos,$id,$seq,$ref,$qual, $filter,$other);
    }else{
        print ;
    }
}