72 lines
1.8 KiB
Perl
Executable File
72 lines
1.8 KiB
Perl
Executable File
#!/usr/bin/perl
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use strict;
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use warnings;
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die "usage:perl $0 germline/somatic sample_type name input_file output_file" unless @ARGV == 5;
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my ($type, $sample_type, $name, $input, $output) = @ARGV;
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open IN, $input or die "Cannot open file $input: $!";
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open OUT, ">${output}";
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if ($type eq "germline") {
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while (<IN>) {
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if (/^##/) {
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print OUT;
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next;
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}
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elsif (/^#CHROM/) {
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$_ =~ s/TUMOR/$name/;
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print OUT;
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next;
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}
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else {
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chomp;
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my @line = split("\t", $_);
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next if $line[6] ne "PASS";
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if ($sample_type eq 'c') {
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my $n_af = (split(":", $line[-1]))[6];
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print OUT "$_\n" if $n_af >= 0.1;
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}
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else {
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my $n_af = (split(":", $line[-1]))[6];
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my $t_af = (split(":", $line[-2]))[6];
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print OUT "$_\n" if ($n_af >= 0.1 and $t_af >= 0.1);
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}
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}
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}
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}
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elsif ($type eq "somatic") {
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while (<IN>) {
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if (/^##/) {
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print OUT;
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next;
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}
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elsif (/^#CHROM/) {
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$_ =~ s/TUMOR/$name/;
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print OUT;
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next;
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}
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else {
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chomp;
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my @line = split("\t", $_);
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next if $line[6] ne "PASS";
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if ($sample_type eq 'c') {
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my $t_af = (split(":", $line[-1]))[6];
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print OUT "$_\n" if $t_af >= 0.02;
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}
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else {
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my $n_af = (split(":", $line[-1]))[6];
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my $t_af = (split(":", $line[-2]))[6];
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print OUT "$_\n" if ($n_af < 0.02 and $t_af >= 0.05);
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}
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}
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}
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}
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else {
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die "erro type!!! somatic or germline for now"
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}
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