--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snp_analysis_conversion/vcf2pgSnpMult.pl	Tue May 28 17:01:14 2013 -0400
@@ -0,0 +1,81 @@
+#!/usr/bin/perl -w
+use strict;
+
+#convert from a vcf file to a pgSnp file with multiple sets of the allele
+# specific columns
+#frequency count = chromosome count
+
+my $in;
+my $stCol = 9;
+my $endCol;
+if (@ARGV && scalar @ARGV == 1) {
+   $in = shift @ARGV;
+}else {
+   print "usage: vcf2pgSnpMult.pl file.vcf > file.pgSnpMult\n";
+   exit;
+}
+
+if ($in =~ /.gz$/) {
+   open(FH, "zcat $in |") or die "Couldn't open $in, $!\n";
+}else {
+   open(FH, $in) or die "Couldn't open $in, $!\n";
+}
+while (<FH>) {
+   chomp; 
+   if (/^\s*#/) { next; } #skip comments/headers
+   if (/^\s*$/) { next; } #skip blank lines
+   my @f = split(/\t/);
+   #chr pos1base ID refNt altNt[,|D#|Int] quality filter info format geno1 ...
+   my $a;
+   my %nt;
+   my %all;
+   my $cnt = 0;
+   my $var;
+   if ($f[3] eq 'N') { next; } #ignore ref=N
+   if ($f[4] =~ /[DI]/ or $f[3] =~ /[DI]/) { next; } #don't do microsatellite
+   if ($f[6] && !($f[6] eq '.' or $f[6] eq 'PASS')) { next; } #filtered for some reason
+   my $ind = 0;
+   if ($f[8] ne 'GT') { #more than just genotype
+      my @t = split(/:/, $f[8]);
+      foreach (@t) { if ($_ eq 'GT') { last; } $ind++; }
+      if ($ind == 0 && $f[8] !~ /^GT/) { die "ERROR couldn't find genotype in format $f[8]\n"; }
+   }
+   if (!$endCol) { $endCol = $#f; }
+   #put f[3] => nt{0} and split f[4] for rest of nt{}
+   $nt{0} = $f[3];
+   my @t = split(/,/, $f[4]);
+   for (my $i=0; $i<=$#t; $i++) {
+      my $j = $i + 1;
+      $nt{$j} = $t[$i];
+   }
+   if ($f[0] !~ /chr/) { $f[0] = "chr$f[0]"; }
+   print "$f[0]\t", ($f[1]-1), "\t$f[1]"; #position info
+   foreach my $col ($stCol .. $endCol) {  #add each individual (4 columns)
+      if ($ind > 0) { 
+         my @t = split(/:/, $f[$col]);
+         $f[$col] = $t[$ind] . ":"; #only keep genotype part
+      }
+      print "\t";
+      if ($f[$col] =~ /^(\d).(\d)/) {
+          my $a1 = $1;
+          my $a2 = $2;
+          if (!exists $nt{$a1}) { die "ERROR bad allele $a1 in $f[3] $f[4]\n"; }
+          if (!exists $nt{$a2}) { die "ERROR bad allele $a2 in $f[3] $f[4]\n"; }
+          if ($a1 eq $a2) { #homozygous
+             print "$nt{$a1}\t1\t2\t0"; 
+          }else { #heterozygous
+             print "$nt{$a1}/$nt{$a2}\t2\t1,1\t0,0";
+          } 
+      }elsif ($f[$col] =~ /^(\d):/) { #chrY or male chrX, single
+          my $a1 = $1;
+          if (!exists $nt{$a1}) { die "ERROR bad allele $a1 in $f[3] $f[4]\n"; }
+          print "$nt{$a1}\t1\t1\t0";
+      }else { #don't know how to parse
+          die "ERROR unknown genotype $f[$col]\n";
+      }
+   }
+   print "\n"; #end this SNP
+}
+close FH;
+
+exit;