annotate SNV/filter_snvmix.pl @ 5:a4975ec34575

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#!/usr/bin/perl
use strict;
use Getopt::Std;
use vars qw($opt_d $opt_p $opt_c $opt_C $opt_i $opt_S $opt_P $opt_I);
getopts("d:cC:i:p:SPI:");

my $usage = "$0 -p nonref_p-value_threshold [0.99] -c track_sequenced_bases -d minimum_nonref_depth [2] -C minimum_number_of_read_centered_calls [1] -i max_num_indels [0] -S need_dual_strand_coverage [0] -P use_unpaired_reads_too";

#chr:pos ref nref ref:ref_count,nref:nref_count,pAA,pAB,pBB,maxPr+ r- n+ n- nC nE nD
#chr:pos ref nref ref:ref_count,nref:nref_count,pAA,pAB,pBB,maxP ref_fwd ref_rev nref_fwd nref_rev       nref_center nref_edges  indel_pos       ref_clean nref_clean    ref_bad_pair nref_bad_pair      ref_ins nref_ins        ref_del nref_del   ref_junc nref_junc      nref_in_unique_pos
my $nonref_depth_thresh = $opt_d || 2;
my $min_centered = $opt_C || 1;
my $max_indels = $opt_i || 0;
my $dual_strand = $opt_S;
my $p_threshold = $opt_p || 0.99;
my $track_sequenced_bases = $opt_c;
my $pair_filtering = 1;
my $max_indel_relative = $opt_I;  #filter on proportion of indels at SNV position relative to nonref calls. E.g. 0.5 would allow 1/2 the number of indel reads at that position vs indels.  
if($opt_P){
    $pair_filtering = 0;
}
while(<STDIN>){
    chomp;
    my ($chrpos,$ref,$nonref,$info,$ref_plus,$ref_minus,$nonref_plus,$nonref_minus,$centered,$ended,$indels,$ref_clean,$nonref_clean,$ref_bad_pair,$nonref_bad_pair,$ref_ins,$nonref_ins,$ref_del,$nonref_del,$ref_junc,$nref_junc,$nonref_in_unique_pos) = split;
    my $ok;
    my ($ref_info, $nref_info, $pAA, $pAB, $pBB, $call) = split(/,/, $info);
    my $skip;
    if($track_sequenced_bases){
	$skip = 1 if $call == 1;
    }
    else{
	next if $call == 1;
    }
    my $is_sequenced;
    my ($foo,$nref_num) = split /:/, $nref_info;
    if($pAA < ($pAB + $pBB)) {
	if( ($pAB + $pBB) >= $p_threshold) {
	    $is_sequenced = $pAB+$pBB;
	}
	else{
	    next;
	}
    }   
    else{
	if($track_sequenced_bases){
	    if($pAA >= $p_threshold){
		$is_sequenced = $pAA;
	    }
#	    print STDERR "skip $skip\n";
	    $skip = 1;
	}
	else{
	    next;
	}

    }

    if($track_sequenced_bases){
	if($is_sequenced){
	    print STDERR "$chrpos\t$is_sequenced\n";
	}
	next if $skip;
    }
    if($indels <= $max_indels && $centered >= $min_centered && $nref_num >= $nonref_depth_thresh){
	if($dual_strand){
	    $ok=1 if $nonref_minus > 0 && $nonref_plus > 0;
	}
	else{
	    $ok= 1;
	}
    }
    else{
	#print "$_ FAIL\n$indels <= $max_indels && $centered >= $min_centered && $nref_num >= $nonref_depth_thresh\n";
    }
#    if($nonref_bad_pair > ($nonref_plus+$nonref_minus)/2){
    if($nonref_bad_pair > 1 && $pair_filtering){
        #Rodrigo's bad pair filter fail
        #print STDERR "skipping $chrpos due to $nonref_bad_pair >  ($nonref_plus+$nonref_minus)/2\n";
	$ok = 0;

    }

    unless($chrpos =~ /^chr/){
	$chrpos = "chr$chrpos";
    }
    if($ok){
	print "$chrpos\t$ref\t$nonref\t$info\n";
    }
}