From d5c688e81395f8ea4f166428134331c2fbada9ee Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 5 Aug 2020 16:22:17 -0500
Subject: [PATCH] update checkmate script location
---
cbioportal/concat_cnvs.pl | 18 +++++++++++++++---
variants/checkmate.sh | 4 ++--
2 files changed, 17 insertions(+), 5 deletions(-)
diff --git a/cbioportal/concat_cnvs.pl b/cbioportal/concat_cnvs.pl
index 11fd0aa..1e0f0cc 100644
--- a/cbioportal/concat_cnvs.pl
+++ b/cbioportal/concat_cnvs.pl
@@ -11,7 +11,19 @@ foreach $file (@discreet) {
while (my $line = <IN>) {
chomp($line);
my ($chr,$s,$e,$ct,$gene) = split(/\t/,$line);
- $cts{$gene}{$sample} = $ct;
+ my $discreet = 0;
+ if ($ct == 1) {
+ $discreet = -1;
+ }elsif ($ct == 0) {
+ $discreet = -2;
+ }elsif ($ct == 3) {
+ $discreet = 1;
+ }elsif ($ct > 3) {
+ $discreet = 2;
+ }elsif ($ct eq 'NA') {
+ $ct = '';
+ }
+ $cts{$gene}{$sample} = $discreet;
}
}
my @samples = sort {$a cmp $b} keys %sample;
@@ -20,14 +32,14 @@ print OUT join("\t",'Hugo_Symbol',@samples),"\n";
foreach my $gene (keys %cts) {
my @line;
foreach my $sid (@samples) {
- $cts{$gene}{$sid} = 2 unless ($cts{$gene}{$sid});
+ $cts{$gene}{$sid} = 0 unless (exists $cts{$gene}{$sid});
push @line, $cts{$gene}{$sid};
}
print OUT join("\t",$gene,@line),"\n";
}
my @continuous = `ls *cnv_continuous.txt`;
- my %cts;
+my %cts;
my %sample;
foreach $file (@continuous) {
open IN, "<$file" or die $!;
diff --git a/variants/checkmate.sh b/variants/checkmate.sh
index 193b51f..6bdb0cf 100755
--- a/variants/checkmate.sh
+++ b/variants/checkmate.sh
@@ -50,9 +50,9 @@ for i in *.bam; do
bcftools mpileup -A -d 1000000 -C50 -Ou --gvcf 0 -f ${reffa} -T ${capture} $i | bcftools call -m --gvcf 0 -Ov | bcftools convert --gvcf2vcf -f ${reffa} -Ov -o ${prefix}.vcf
done
-if [[ -f /project/shared/bicf_workflow_ref/seqprg/bin/ncm.py ]]
+if [[ -f /project/shared/bicf_workflow_ref/seqprg/NGSCheckMate/ncm.py ]]
then
- ncm=/project/shared/bicf_workflow_ref/seqprg/bin/ncm.py
+ ncm=/project/shared/bicf_workflow_ref/seqprg/NGSCheckMate/ncm.py
elif [[ -f /usr/local/bin/ncm.py ]]
then
ncm=/usr/local/bin/ncm.py
--
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