hapmap2vcf convertor

diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index b01799f0975dca19c81a17ac2744ccca14050bcf..c625b38d774a9ae8a1ba5d213a497bc9a1f18189 100755 (executable)
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -13,7 +13,8 @@ sub main {
   my $version = '0.1.0';
   &usage if (@ARGV < 1);
   my $command = shift(@ARGV);
-  my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter);
+  my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter,
+                         hapmap2vcf=>\&hapmap2vcf);
   die("Unknown command \"$command\".\n") if (!defined($func{$command}));
   &{$func{$command}};
 }
@@ -130,9 +131,9 @@ Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions #
   for my $p (@a) {
        if ($p->[0] == -1 || ($p->[0] != $last && $c[0]/@a > $next)) {
          my @x;
-         $x[0] = sprintf("%.3f", $c[1]-$c[2]? $c[2] / ($c[1] - $c[2]) : 100);
-         $x[1] = sprintf("%.3f", $hsize? $c[3] / $hsize : 0);
-         $x[2] = sprintf("%.3f", $c[3] / $c[1]);
+         $x[0] = sprintf("%.4f", $c[1]-$c[2]? $c[2] / ($c[1] - $c[2]) : 100);
+         $x[1] = sprintf("%.4f", $hsize? $c[3] / $hsize : 0);
+         $x[2] = sprintf("%.4f", $c[3] / $c[1]);
          print join("\t", $last, @c, @x), "\n";
          $next = $c[0]/@a + $opts{s};
        }
@@ -281,6 +282,58 @@ sub varFilter_aux {
   }
 }
 
+sub hapmap2vcf {
+  die("Usage: vcfutils.pl <in.ucsc.snp> <in.hapmap>\n") if (@ARGV == 0);
+  my $fn = shift(@ARGV);
+  # parse UCSC SNP
+  warn("Parsing UCSC SNPs...\n");
+  my ($fh, %map);
+  open($fh, ($fn =~ /\.gz$/)? "gzip -dc $fn |" : $fn) || die;
+  while (<$fh>) {
+       my @t = split;
+       next if ($t[3] - $t[2] != 1); # not SNP
+       @{$map{$t[4]}} = @t[1,3,7];
+  }
+  close($fh);
+  # write VCF
+  warn("Writing VCF...\n");
+  print "##fileformat=VCFv4.0\n";
+  while (<>) {
+       my @t = split;
+       if ($t[0] eq 'rs#') { # the first line
+         print join("\t", "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", @t[11..$#t]), "\n";
+       } else {
+         next unless ($map{$t[0]});
+         next if (length($t[1]) != 3); # skip non-SNPs
+         my $a = \@{$map{$t[0]}};
+         my $ref = $a->[2];
+         my @u = split('/', $t[1]);
+         if ($u[1] eq $ref) {
+               $u[1] = $u[0]; $u[0] = $ref;
+         } elsif ($u[0] ne $ref) { next; }
+         my $alt = $u[1];
+         my %w;
+         $w{$u[0]} = 0; $w{$u[1]} = 1;
+         my @s = (@$a[0,1], $t[0], $ref, $alt, 0, '.', '.', 'GT');
+         my $is_tri = 0;
+         for (@t[11..$#t]) {
+               if ($_ eq 'NN') {
+                 push(@s, './.');
+               } else {
+                 my @a = ($w{substr($_,0,1)}, $w{substr($_,1,1)});
+                 if (!defined($a[0]) || !defined($a[1])) {
+                       $is_tri = 1;
+                       last;
+                 }
+                 push(@s, "$a[0]/$a[1]");
+               }
+         }
+         next if ($is_tri);
+         print join("\t", @s), "\n";
+       }
+  }
+}
+
 sub usage {
   die(qq/
 Usage:   vcfutils.pl <command> [<arguments>]\n
@@ -289,5 +342,6 @@ Command: subsam       get a subset of samples
          fillac       fill the allele count field
          qstats       SNP stats stratified by QUAL
          varFilter    filtering short variants
+         hapmap2vcf   convert the hapmap format to VCF
 \n/);
 }