&usage if (@ARGV < 1);
my $command = shift(@ARGV);
my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter,
- hapmap2vcf=>\&hapmap2vcf, ucscsnp2vcf=>\&ucscsnp2vcf);
+ hapmap2vcf=>\&hapmap2vcf, ucscsnp2vcf=>\&ucscsnp2vcf, filter4vcf=>\&filter4vcf);
die("Unknown command \"$command\".\n") if (!defined($func{$command}));
&{$func{$command}};
}
}
}
+sub filter4vcf {
+ my %opts = (d=>3, D=>2000, 1=>1e-4, 2=>1e-100, 3=>0, 4=>1e-4, Q=>10, q=>3);
+ getopts('d:D:1:2:3:4:Q:q:', \%opts);
+ die(qq/
+Usage: vcfutils.pl filter4vcf [options] <in.vcf>
+
+Options: -d INT min total depth (given DP or DP4) [$opts{D}]
+ -D INT max total depth [$opts{d}]
+ -q INT min SNP quality [$opts{q}]
+ -Q INT min RMS mapQ (given MQ) [$opts{Q}]
+ -1 FLOAT min P-value for strand bias (given PV4) [$opts{1}]
+ -2 FLOAT min P-value for baseQ bias [$opts{2}]
+ -3 FLOAT min P-value for mapQ bias [$opts{3}]
+ -4 FLOAT min P-value for end distance bias [$opts{4}]\n
+/) if (@ARGV == 0 && -t STDIN);
+
+ my %ts = (AG=>1, GA=>1, CT=>1, TC=>1);
+
+ my @n = (0, 0);
+ while (<>) {
+ next if (/^#/);
+ next if (/PV4=([^,]+),([^,]+),([^,]+),([^,;\t]+)/ && ($1<$opts{1} || $2<$opts{2} || $3<$opts{3} || $4<$opts{4}));
+ my $depth = -1;
+ $depth = $1 if (/DP=(\d+)/);
+ $depth = $1+$2+$3+$4 if (/DP4=(\d+),(\d+),(\d+),(\d+)/);
+ next if ($depth > 0 && ($depth < $opts{d} || $depth > $opts{D}));
+ next if (/MQ=(\d+)/ && $1 < $opts{Q});
+ my @t = split;
+ next if ($t[5] >= 0 && $t[5] < $opts{q});
+ ++$n[0];
+ my @s = split(',', $t[4]);
+ ++$n[1] if ($ts{$t[3].$s[0]});
+ print;
+ }
+}
+
sub ucscsnp2vcf {
die("Usage: vcfutils.pl <in.ucsc.snp>\n") if (@ARGV == 0 && -t STDIN);
print "##fileformat=VCFv4.0\n";
fillac fill the allele count field
qstats SNP stats stratified by QUAL
varFilter filtering short variants
+ filter4vcf filtering VCFs produced by samtools+bcftools
hapmap2vcf convert the hapmap format to VCF
ucscsnp2vcf convert UCSC SNP SQL dump to VCF
\n/);