--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snp_analysis_conversion/vcf2pgSnp.pl	Tue May 28 17:01:14 2013 -0400
@@ -0,0 +1,116 @@
+#!/usr/bin/perl -w
+use strict;
+
+#convert from a vcf file to a pgSnp file. 
+#frequency count = chromosome count
+#either a single column/individual 
+#or all columns as a population 
+
+my $in;
+my $stCol = 9;
+my $endCol;
+if (@ARGV && scalar @ARGV == 2) {
+   $stCol = shift @ARGV;
+   $in = shift @ARGV;
+   if ($stCol eq 'all') { $stCol = 10; }
+   else { $endCol = $stCol; }
+   $stCol--; #go from 1 based to zero based column number
+   if ($stCol < 9) { 
+      print "ERROR genotype fields don't start until column 10\n";
+      exit;
+   }
+}elsif (@ARGV && scalar @ARGV == 1) {
+   $in = shift @ARGV;
+}elsif (@ARGV) {
+   print "usage: vcf2pgSnp.pl [indColNum default=all] file.vcf > file.pgSnp\n";
+   exit;
+}
+
+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[4] =~ /[ACTG],[ACTG]/) { next; } #only do positions with single alternate
+   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 $f[8]\n"; }
+   }
+   #count 0's, 1's, 2's
+   if (!$endCol) { $endCol = $#f; }
+   foreach my $col ($stCol .. $endCol) {
+      if ($ind > 0) { 
+         my @t = split(/:/, $f[$col]);
+         $f[$col] = $t[$ind] . ":"; #only keep genotype part
+      }
+      if ($f[$col] =~ /^(0|1|2).(0|1|2)/) {
+         $nt{$1}++;
+         $nt{$2}++;
+      }elsif ($f[$col] =~ /^(0|1|2):/) { #chrY or male chrX, single
+         $nt{$1}++;
+      } #else ignore
+   }
+   if (%nt) {
+      if ($f[0] !~ /chr/) { $f[0] = "chr$f[0]"; }
+      print "$f[0]\t", ($f[1]-1), "\t$f[1]\t"; #position info
+      my $cnt = scalar(keys %nt);
+      my $fr;
+      my $sc;
+      my $all;
+      if (exists $nt{0}) {
+         $all = uc($f[3]);
+         $fr = $nt{0};
+         $sc = 0;
+      }
+      if (!exists $nt{0} && exists $nt{1}) {
+         if ($f[4] =~ /([ACTG]),?/) {
+            $all = $1;
+            $fr = $nt{1};
+            $sc = 0;
+         }else { die "bad variant nt $f[4] for nt 1"; }
+      }elsif (exists $nt{1}) {
+         if ($f[4] =~ /([ACTG]),?/) {
+            $all .= '/' . $1;
+            $fr .= ",$nt{1}";
+            $sc .= ",0";
+         }else { die "bad variant nt $f[4] for nt 1"; }
+      }
+      if (exists $nt{2}) {
+         if ($f[4] =~ /^[ACTG],([ACTG]),?/) {
+            $all .= '/' . $1;
+            $fr .= ",$nt{2}";
+            $sc .= ",0";
+         }else { die "bad variant nt $f[4] for nt 2"; }
+      }
+      if (exists $nt{3}) {
+         if ($f[4] =~ /^[ACTG],[ACTG],([ACTG])/) {
+            $all .= '/' . $1;
+            $fr .= ",$nt{3}";
+            $sc .= ",0";
+         }else { die "bad variant nt $f[4] for nt 3"; }
+      }
+      if (exists $nt{4}) {
+         if ($f[4] =~ /^[ACTG],[ACTG],[ACTG],([ACTG])/) {
+            $all .= '/' . $1;
+            $fr .= ",$nt{4}";
+            $sc .= ",0";
+         }else { die "bad variant nt $f[4] for nt 4"; }
+      }
+      print "$all\t$cnt\t$fr\t$sc\n";
+   }
+}
+close FH;
+
+exit;