/
merge_gatk.pl
77 lines (62 loc) · 2.2 KB
/
merge_gatk.pl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
#!/usr/bin/perl
### snv: union call from varscan and gatk
### indel: callings from pindel or both gatak and varscan
use strict;
use warnings;
die unless @ARGV == 2;
my @chrlist=("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X","Y");
my ($sample_full_path,$sample_name)=@ARGV;
my $f_snv;
my $f_indel;
my $f_snv_idx;
my $f_indel_idx;
my $f_gvip;
my $f_gvip_idx;
my $f_snv_out=$sample_full_path."/gatk/".$sample_name.".snv.gvip.vcf";
my $f_ind_out=$sample_full_path."/gatk/".$sample_name.".indel.gvip.vcf";
open(OUT1,">$f_snv_out");
open(OUT2,">$f_ind_out");
foreach my $chr (@chrlist)
{
$f_snv=$sample_full_path."/gatk/".$sample_name.".snv.gvip.$chr.vcf";
$f_indel=$sample_full_path."/gatk/".$sample_name.".indel.gvip.$chr.vcf";
$f_snv_idx=$sample_full_path."/gatk/".$sample_name.".snv.gvip.$chr.vcf.idx";
$f_indel_idx=$sample_full_path."/gatk/".$sample_name.".indel.gvip.$chr.vcf.idx";
$f_gvip=$sample_full_path."/gatk/".$sample_name.".gvip.$chr.vcf";
$f_gvip_idx=$sample_full_path."/gatk/".$sample_name.".gvip.$chr.vcf.idx";
#$f_raw_idx=$sample_full_path."/gatk/".$sample_name.".gvip.$chr.vcf.idx";
#$f_raw=$sample_full_path."/gatk/".$sample_name.".snv.gvip.$chr.vcf";
if(-e $f_snv)
{
foreach my $l (`cat $f_snv`)
{
my $ltr=$l;
chomp($ltr);
if($ltr=~/^#/ && !($chr eq "1")) { next; }
else { print OUT1 $ltr,"\n"; }
}
`rm $f_snv`;
`rm $f_snv_idx`;
}
if(-e $f_indel)
{
foreach my $l (`cat $f_indel`)
{
my $ltr=$l;
chomp($ltr);
if($ltr=~/^#/ && !($chr eq "1")) { next; }
else { print OUT2 $ltr,"\n"; }
}
`rm $f_indel`;
`rm $f_indel_idx`;
}
`rm $f_gvip`;
#`rm $f_raw`;
#`rm $f_raw_idx`;
`rm $f_gvip_idx`;
#print GATK "rawvcf=".$sample_full_path."/gatk/".$sample_name.".raw.$chr.vcf\n";
#print GATK "gvipvcf=".$sample_full_path."/gatk/".$sample_name.".gvip.$chr.vcf\n";
#print GATK "snvvcf=".$sample_full_path."/gatk/".$sample_name.".snv.gvip.$chr.vcf\n";
#print GATK "indelvcf=".$sample_full_path."/gatk/".$sample_name.".indel.gvip.$chr.vcf\n";
#print GATK " ".$run_script_path."genomevip_label.pl GATK \${rawvcf} \${gvipvcf}"."\n";
}