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
|
#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\n\tusage: $0 samples_file dir/containing/bams\n\n";
my $samples_file = $ARGV[0] or die $usage;
my $bam_dir_path = $ARGV[1] or die $usage;
my %tissue_id_to_bams;
open(my $fh, $samples_file) or die $!;
while(<$fh>) {
chomp;
my ($tissue_type, $sample_id, @rest) = split(/\t/);
my @bams = <$bam_dir_path/$sample_id.*.bam>;
unless (scalar(@bams) == 1) {
die "Error, cannot find bam corresping to $bam_dir_path/$sample_id.*.bam ";
}
push (@{$tissue_id_to_bams{$tissue_type}}, $bams[0]);
}
close $fh;
foreach my $tissue_id (keys %tissue_id_to_bams) {
my @bams = @{$tissue_id_to_bams{$tissue_id}};
my $cmd = "samtools merge $tissue_id.bam @bams";
print "$cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, $cmd died with ret $ret";
}
}
exit(0)
|
