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SNPStatv2.pl
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SNPStatv2.pl
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#!/usr/bin/perl
use strict;
my $file=shift;
my $DP_cutoff=shift;
open IN,"< $file" or die $!;
my @array;
while(<IN>){
next if(/^##/);
chomp;
my @line=split(/\t/,$_);
if(/^#CHROM/){
for(my $i=9;$i<@line;$i++){
push @array,[$line[$i],0,0,0,0];
# Sample, Missing, HomoRef, Heter, HomoAlt
}
}else{
for(my $j=9;$j<@line;$j++){
my @tmp=split(/:/,$line[$j]);
if($tmp[2] <5){
$array[$j-9][1]++; # Define as missing if DP <5
}else{
if($tmp[0] eq '0/0'){
$array[$j-9][2]++;
}elsif($tmp[0] eq '0/1'){
$array[$j-9][3]++;
}elsif($tmp[0] eq '1/1'){
$array[$j-9][4]++;
}
}
}
}
}
close IN;
print "Sample\tMissing\tHomoRef\tHeter\tHomoAlt\tTotal_loci\tTotal_call\tHeter_rate_a\tHeter_rate_b\tMissing_rate\n";
for(my $k=0;$k<@array;$k++){
print join("\t",@{$array[$k]});
my $total=$array[$k][1]+$array[$k][2]+$array[$k][3]+$array[$k][4];
my $total_call=$array[$k][2]+$array[$k][3]+$array[$k][4];
my $Heter_rate_a=($array[$k][3]/$total)*100;
$Heter_rate_a=sprintf("%.2f",$Heter_rate_a);
my $Heter_rate_b=($array[$k][3]/$total_call)*100;
$Heter_rate_b=sprintf("%.2f",$Heter_rate_b);
my $Missing_rate=($array[$k][1]/$total)*100;
$Missing_rate=sprintf("%.2f",$Missing_rate);
print "\t$total\t$total_call\t$Heter_rate_a\t$Heter_rate_b\t$Missing_rate\n";
}