* samtools-0.1.9-8 (r807)

[samtools.git] / bcftools / vcfutils.pl

diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index 0cf73a30d640f6e0747e2cc4b9af8e4bbfb815a7..c1177eacb9603cc2cb9f93ab27d54b5add1e0779 100755 (executable)
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -10,11 +10,10 @@ use Getopt::Std;
 exit;
 
 sub main {
-  my $version = '0.1.0';
   &usage if (@ARGV < 1);
   my $command = shift(@ARGV);
   my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter,
-                         hapmap2vcf=>\&hapmap2vcf, ucscsnp2vcf=>\&ucscsnp2vcf, filter4vcf=>\&filter4vcf, ldstats=>\&ldstats);
+                         hapmap2vcf=>\&hapmap2vcf, ucscsnp2vcf=>\&ucscsnp2vcf, filter4vcf=>\&varFilter, ldstats=>\&ldstats);
   die("Unknown command \"$command\".\n") if (!defined($func{$command}));
   &{$func{$command}};
 }
@@ -199,8 +198,8 @@ Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions #
 }
 
 sub varFilter {
-  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);
+  my %opts = (d=>2, D=>10000, a=>2, W=>10, Q=>10, w=>10, p=>undef, 1=>1e-4, 2=>1e-100, 3=>0, 4=>1e-4);
+  getopts('pd:D:W:Q:w:a:1:2:3:4:', \%opts);
   die(qq/
 Usage:   vcfutils.pl varFilter [options] <in.vcf>
 
@@ -209,19 +208,28 @@ Options: -Q INT    minimum RMS mapping quality for SNPs [$opts{Q}]
          -D INT    maximum read depth [$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 [$opts{l}]
+         -W INT    window size for filtering adjacent gaps [$opts{W}]
+         -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}]
          -p        print filtered variants
+
+Note: Some of the filters rely on annotations generated by SAMtools\/BCFtools.
 \n/) if (@ARGV == 0 && -t STDIN);
 
   # calculate the window size
-  my ($ol, $ow) = ($opts{l}, $opts{w});
+  my ($ol, $ow) = ($opts{W}, $opts{w});
   my $max_dist = $ol > $ow? $ol : $ow;
   # the core loop
   my @staging; # (indel_filtering_score, flt_tag, indel_span; chr, pos, ...)
   while (<>) {
        my @t = split;
-       next if (/^#/);
+    if (/^#/) {
+         print; next;
+       }
        next if ($t[4] eq '.'); # skip non-var sites
+       # check if the site is a SNP
        my $is_snp = 1;
        if (length($t[3]) > 1) {
          $is_snp = 0;
@@ -238,7 +246,6 @@ Options: -Q INT    minimum RMS mapping quality for SNPs [$opts{Q}]
          varFilter_aux(shift(@staging), $opts{p}); # calling a function is a bit slower, not much
        }
        my $flt = 0;
-
        # parse annotations
        my ($dp, $mq, $dp_alt) = (-1, -1, -1);
        if ($t[7] =~ /DP=(\d+)/i) {
@@ -258,6 +265,8 @@ Options: -Q INT    minimum RMS mapping quality for SNPs [$opts{Q}]
        }
        $flt = 4 if ($dp_alt >= 0 && $dp_alt < $opts{a});
        $flt = 1 if ($flt == 0 && $mq >= 0 && $mq < $opts{Q});
+       $flt = 7 if ($flt == 0 && /PV4=([^,]+),([^,]+),([^,]+),([^,;\t]+)/
+                                && ($1<$opts{1} || $2<$opts{2} || $3<$opts{3} || $4<$opts{4}));
 
        # site dependent filters
        my ($rlen, $indel_score) = (0, -1); # $indel_score<0 for SNPs
@@ -300,46 +309,7 @@ sub varFilter_aux {
   if ($first->[1] == 0) {
        print join("\t", @$first[3 .. @$first-1]), "\n";
   } elsif ($is_print) {
-       print STDERR join("\t", substr("UQdDaGgsiX", $first->[1], 1), @$first[3 .. @$first-1]), "\n";
-  }
-}
-
-sub filter4vcf {
-  my %opts = (d=>3, D=>2000, 1=>1e-4, 2=>1e-100, 3=>0, 4=>1e-4, Q=>10, q=>3);
-  getopts('d:D:1:2:3:4:Q:q:', \%opts);
-  die(qq/
-Usage:   vcfutils.pl filter4vcf [options] <in.vcf>
-
-Options: -d INT     min total depth (given DP or DP4) [$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 (<>) {
-       if (/^#/) {
-         print;
-         next;
-       }
-       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;
+       print STDERR join("\t", substr("UQdDaGgP", $first->[1], 1), @$first[3 .. @$first-1]), "\n";
   }
 }
 
@@ -436,7 +406,6 @@ Command: subsam       get a subset of samples
          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/);