added filter for samtools/bcftools genetated VCFs

diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index cdb96cb53ee287fbbc3b541baa50c7778ec176bb..0506c5dbacb4e4480eebf4eab5990787d423c7f9 100755 (executable)
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -14,7 +14,7 @@ sub main {
   &usage if (@ARGV < 1);
   my $command = shift(@ARGV);
   my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter,
   &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{$command}};
 }
   die("Unknown command \"$command\".\n") if (!defined($func{$command}));
   &{$func{$command}};
 }


@@ -316,6 +316,42 @@ sub varFilter_aux {
   }
 }
 
   }
 }
 

+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";
 sub ucscsnp2vcf {
   die("Usage: vcfutils.pl <in.ucsc.snp>\n") if (@ARGV == 0 && -t STDIN);
   print "##fileformat=VCFv4.0\n";


@@ -409,6 +445,7 @@ Command: subsam       get a subset of samples
          fillac       fill the allele count field
          qstats       SNP stats stratified by QUAL
          varFilter    filtering short variants
          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/);
          hapmap2vcf   convert the hapmap format to VCF
          ucscsnp2vcf  convert UCSC SNP SQL dump to VCF
 \n/);