From 07dfaba50cbacd8b018bd65d08901f845018d99f Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Sun, 20 Sep 2020 15:29:05 -0500
Subject: [PATCH] alter pindel filtering
---
variants/filter_pindel.pl | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/variants/filter_pindel.pl b/variants/filter_pindel.pl
index 1802a79..0048d75 100755
--- a/variants/filter_pindel.pl
+++ b/variants/filter_pindel.pl
@@ -43,7 +43,7 @@ foreach $file (@files) {
$hash{$key} = $val unless ($hash{$key});
}
next unless ($hash{ANN});
- next unless ($hash{ANN} =~ m/HIGH|MODERATE|LOW/);
+ #next unless ($hash{ANN} =~ m/HIGH|MODERATE|LOW/);
my %gtinfo = ();
my @deschead = split(/:/,$format);
F1:foreach my $k (0..$#gtheader) {
@@ -79,15 +79,15 @@ foreach $file (@files) {
@tumoraltct = split(/,/,$gtinfo{$opt{tumor}}{AO});
next if ($tumoraltct[0] eq '.');
$hash{AF} = join(",",@tumormaf);
- next if ($tumoraltct[0] < 20);
+ next if ($tumoraltct[0] < 20 && $tumormaf[0] < 0.05);
next if ($tumormaf[0] < 0.01);
my $keepforvcf = 0;
foreach $trx (split(/,/,$hash{ANN})) {
my ($allele,$effect,$impact,$gene,$geneid,$feature,
$featureid,$biotype,$rank,$codon,$aa,$pos_dna,$len_cdna,
$cds_pos,$cds_len,$aapos,$aalen,$distance,$err) = split(/\|/,$trx);
- next unless ($impact =~ m/HIGH|MODERATE/ || $effect =~ /splice/i);
- next if($effect eq 'sequence_feature');
+ #next unless ($impact =~ m/HIGH|MODERATE/ || $effect =~ /splice/i);
+ #next if($effect eq 'sequence_feature');
$keepforvcf = $gene;
}
next unless $keepforvcf;
--
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