From 018b4abf161b05d6fb67cc6267f0b92180e9a3c9 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 30 Apr 2020 11:46:39 -0500
Subject: [PATCH] fitler virus, filter cna
---
alignment/virusalign.sh | 2 +-
variants/filter_cnvkit.pl | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/alignment/virusalign.sh b/alignment/virusalign.sh
index 1158137..6343ef9 100644
--- a/alignment/virusalign.sh
+++ b/alignment/virusalign.sh
@@ -49,5 +49,5 @@ samtools index ${pairid}.viral.bam
samtools idxstats ${pairid}.viral.bam >${pairid}.viral.idxstats.txt
if [[ $filter == 1 ]]
then
- perl $baseDir/filter_viral_idxstats.txt -p ${pairid} ${pairid}.viral.idxstats.txt
+ perl $baseDir/filter_viral_idxstats.pl -p ${pairid} ${pairid}.viral.idxstats.txt
fi
diff --git a/variants/filter_cnvkit.pl b/variants/filter_cnvkit.pl
index 86545f5..772feaf 100755
--- a/variants/filter_cnvkit.pl
+++ b/variants/filter_cnvkit.pl
@@ -54,7 +54,7 @@ while (my $line = <CNR>) {
} else {
my @ids = split(/,/,$geneids);
foreach my $gid (@ids) {
- next if ($gid =~ /^rs\d+$|^SNP:rs\d+$|^-$|Fusion/);
+ next if ($gid =~ /^rs\d+$|^SNP:rs\d+$|^-$|Fusion|MSI/);
my ($gene,@other) = split(/:/,$gid);
my ($gname,@loc) = split(/_/,$gene);
$genes{$gname} = 1;
@@ -93,7 +93,7 @@ while (my $line = <IN>) {
} else {
my @ids = split(/,/,$geneids);
foreach my $gid (@ids) {
- next if ($gid =~ /^rs\d+$|^SNP:rs\d+$|^-$|Fusion/);
+ next if ($gid =~ /^rs\d+$|^SNP:rs\d+$|^-$|Fusion|MSI/);
my ($gene,@other) = split(/:/,$gid);
my ($gname,@loc) = split(/_/,$gene);
$genes{$gname} = 1;
--
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