From 004badb3a7a206395b636f3c3f5df15c93cc1134 Mon Sep 17 00:00:00 2001 From: Heng Li 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] 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