From f98571cb2d62b72d92ec3ef5ba2b8f4dd0b6d8af Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 4 Apr 2019 14:55:00 -0500
Subject: [PATCH] update filter pindel.pl
---
variants/filter_pindel.pl | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/variants/filter_pindel.pl b/variants/filter_pindel.pl
index efc9a5c..c8769e7 100644
--- a/variants/filter_pindel.pl
+++ b/variants/filter_pindel.pl
@@ -80,7 +80,6 @@ foreach $file (@files) {
next if ($tumoraltct[0] eq '.');
$hash{AF} = join(",",@tumormaf);
next if ($tumoraltct[0] < 20);
- next if ($tumormaf[0] < 0.05);
my $keepforvcf = 0;
foreach $trx (split(/,/,$hash{ANN})) {
my ($allele,$effect,$impact,$gene,$geneid,$feature,
@@ -94,6 +93,9 @@ foreach $file (@files) {
$keepforvcf = $gene;
}
next unless $keepforvcf;
+ if ($tumormaf[0] < 0.1) {
+ next unless ($outfile =~ m/pindel_tandemdup/);
+ }
my @fail = sort {$a cmp $b} keys %fail;
next if (scalar(@fail) > 0);
my @nannot;
--
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