From 8434932052bd573532f22a0db1acc35985e36adb Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 18 Jul 2018 17:03:15 -0500
Subject: [PATCH] updates pipeline
---
variants/cnvkit.sh | 2 +-
variants/unionvcf.pl | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/variants/cnvkit.sh b/variants/cnvkit.sh
index a914b34..4b2513c 100755
--- a/variants/cnvkit.sh
+++ b/variants/cnvkit.sh
@@ -61,5 +61,5 @@ cnvkit.py coverage ${sbam} ${targets}antitargets.bed -o ${pair_id}.antitargetcov
cnvkit.py fix ${pair_id}.targetcoverage.cnn ${pair_id}.antitargetcoverage.cnn ${normals} -o ${pair_id}.cnr
cnvkit.py segment ${pair_id}.cnr -o ${pair_id}.cns
cnvkit.py call ${pair_id}.cns -o ${pair_id}.call.cns
-cnvkit.py scatter ${pair_id}.cnr -s ${pair_id}.call.cns -o ${pair_id}.cnv.scatter.pdf
+cnvkit.py scatter ${pair_id}.cnr -s ${pair_id}.call.cns -t --segment-color "blue" -o ${pair_id}.cnv.scatter.pdf
perl $baseDir/filter_cnvkit.pl *.call.cns
diff --git a/variants/unionvcf.pl b/variants/unionvcf.pl
index 6ef3475..ee84efb 100755
--- a/variants/unionvcf.pl
+++ b/variants/unionvcf.pl
@@ -97,7 +97,7 @@ foreach $vcf (@vcffiles) {
}
my $mafs = '.';
my @maf = ();
- if ($gtdata{DP} && $gtdata{DP} ne '.' && $gtdata{AO} && $gtdata{AO} ne '.') {
+ if ($gtdata{DP} && $gtdata{DP} ne '.' && exists $gtdata{AO} && $gtdata{AO} ne '.') {
foreach $areadct (split(/,/,$gtdata{AO})) {
push @maf, sprintf("%.2f",$areadct/$gtdata{DP});
}
--
GitLab