From 3b032697a4be7a72e80055bf40e7b08fc1f74a61 Mon Sep 17 00:00:00 2001
From: Tobias Marschall <tobias.marschall@0ohm.net>
Date: Fri, 19 Oct 2018 17:31:11 +0200
Subject: [PATCH] Jan's update to filter scripts.
---
utils/filter_MosaiCatcher_calls.pl | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/utils/filter_MosaiCatcher_calls.pl b/utils/filter_MosaiCatcher_calls.pl
index e2687c4..506b8d3 100755
--- a/utils/filter_MosaiCatcher_calls.pl
+++ b/utils/filter_MosaiCatcher_calls.pl
@@ -2,7 +2,7 @@
use strict;
my $min_N_inv = 3;
-my $min_WC = 0.2;
+my $min_WC = 1/3;
my $safe_llr_to_ref = 50;
my $SegDup_file = "./utils/segdups/segDups_hg38_UCSCtrack.bed.gz";
my $MaxSegDup_overlap = 0.5;
@@ -17,8 +17,8 @@ my $input_file = $ARGV[0];
if (!$ARGV[0]) {
print STDERR "Input filname missinf=g (use e.g. sv_calls_txt_file_all/RPE1-WT/100000_fixed_norm.selected_j0.01_s0.1/simpleCalls_llr4_poppriorsTRUE_haplotagsTRUE_gtcutoff0.05_regfactor6.txt )\n";
print STDERR "Filters inversions unless they are seen at least $min_N_inv times.\n";
- print STDERR "Filters deletions seen in less then $min_WC WC chromosomes\n";
- print STDERR "Filters duplications seen in less then $min_WC WC chromosomes (but gives inv-dups seen in such context a PASS)\n";
+ print STDERR "Filters deletions seen in not more than $min_WC WC chromosomes\n";
+ print STDERR "Filters duplications seen in not more than $min_WC WC chromosomes (but gives inv-dups seen in such context a PASS)\n";
print STDERR "Del and Dup events with llr_to_ref>=$safe_llr_to_ref will never be masked\n";
printf STDERR "uses SegDup file $SegDup_file and removes all Dels overlapping with SegDups by >%3.1f%\n", $MaxSegDup_overlap*100;
exit;
@@ -193,16 +193,16 @@ foreach my $chrom (sort keys %STARTs) {
$iterate+=$val/@{$FILTER_ARR{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]}};
}
- $FILTER{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]}= sprintf ("FAIL(WC:%4.2f)", $iterate) if ($iterate < $min_WC);
- $FILTER{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]}= "PASS" if ($iterate >= $min_WC or $LLR_TO_REF{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]} >= $safe_llr_to_ref);
+ $FILTER{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]}= sprintf ("FAIL(WC:%4.2f)", $iterate) if ($iterate <= $min_WC);
+ $FILTER{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]}= "PASS" if ($iterate > $min_WC or $LLR_TO_REF{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]} >= $safe_llr_to_ref);
}
if (exists ($TESTED_DUP{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]})) { #check DUP to identify events seen not largely in CC and WW chromosomes
my $iterate=0;
foreach my $val (@{$FILTER_ARR_DUP{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]}}) {
$iterate+=$val/@{$FILTER_ARR_DUP{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]}};
}
- $FILTER{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]}= sprintf ("FAIL(WC:%4.2f)", $iterate) if ($iterate < $min_WC);
- $FILTER{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]}= "PASS" if ($iterate >= $min_WC or $LLR_TO_REF{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]} >= $safe_llr_to_ref);
+ $FILTER{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]}= sprintf ("FAIL(WC:%4.2f)", $iterate) if ($iterate <= $min_WC);
+ $FILTER{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]}= "PASS" if ($iterate > $min_WC or $LLR_TO_REF{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]} >= $safe_llr_to_ref);
}
}
unless (exists($FILTER{$chrom}{$STARTs{$chrom}[$i]}{$ENDs{$chrom}[$i]})) {
--
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