From 004badb3a7a206395b636f3c3f5df15c93cc1134 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Tue, 9 Nov 2010 21:28:39 +0000
Subject: [PATCH] added a double-hit filter to avoid overestimated indel
likelihood
---
bcftools/vcfutils.pl | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index 78f075b..0cf73a3 100755
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -199,14 +199,15 @@ Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions #
}
sub varFilter {
- my %opts = (d=>1, D=>10000, l=>10, Q=>10, s=>100, w=>10, p=>undef, F=>.001);
- getopts('pd:D:l:Q:w:G:F:', \%opts);
+ my %opts = (d=>1, D=>10000, a=>2, l=>10, Q=>10, s=>100, w=>10, p=>undef, F=>.001);
+ getopts('pd:D:l:Q:w:G:F:a:', \%opts);
die(qq/
Usage: vcfutils.pl varFilter [options] <in.vcf>
Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}]
-d INT minimum read depth [$opts{d}]
-D INT maximum read depth [$opts{D}]
+ -a INT minimum number of alternate bases [$opts{a}]
-w INT SNP within INT bp around a gap to be filtered [$opts{w}]
-l INT window size for filtering adjacent gaps [$opts{l}]
-p print filtered variants
@@ -255,6 +256,7 @@ Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}]
$flt = 3;
}
}
+ $flt = 4 if ($dp_alt >= 0 && $dp_alt < $opts{a});
$flt = 1 if ($flt == 0 && $mq >= 0 && $mq < $opts{Q});
# site dependent filters
@@ -298,7 +300,7 @@ sub varFilter_aux {
if ($first->[1] == 0) {
print join("\t", @$first[3 .. @$first-1]), "\n";
} elsif ($is_print) {
- print STDERR join("\t", substr("UQdDWGgsiX", $first->[1], 1), @$first[3 .. @$first-1]), "\n";
+ print STDERR join("\t", substr("UQdDaGgsiX", $first->[1], 1), @$first[3 .. @$first-1]), "\n";
}
}
--
2.39.5