Reduce ctrl_qual_cutoff to one for ALT/HLA contigs

bin/vcf_pileup_compare_allin1_basecount.pl

@@ -25,6 +25,7 @@
 my $tumor = shift;
 my $control = shift;
 my $makeheader = shift;
+my $ctrl_cutoff = shift;
 
 open (T, $tumor) or die "Could not open $tumor: $!\n";
 open (C, $control) or die "Could not open $control: $!\n";
@@ -33,7 +34,7 @@
 # at least 1/30th of reads must support the variant in control to call it germline
 my $fraction = 30;
 # mpileup counts only the bases with score >= 13, so we want to use that cutoff, too
-my $cutoff = 13;
+my $cutoff = $ctrl_cutoff;
 # for RNA, cutoff for calling monoallelic (% of high quality reads). Not 100% bc. of sqcing errors and normal contamination; at least 10 reads
 my $limit = 0.85;
 my $rcutoff = 10;

modules/local/mpileup_compare.nf

@@ -21,6 +21,7 @@ process MPILEUP_COMPARE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def args_c = intervals == "contigs" ? "$args" : "$args -r ${intervals}"
+    def ctrl_qual_cutoff = intervals == "contigs" ? "$ctrl_min_base_qual_contigs" : "$ctrl_min_base_qual"
 
     if (meta.iscontrol == '1' && params.runCompareGermline)
     {

nextflow.config

@@ -37,6 +37,10 @@ params {
     vep_cache                  = null  // No directory for VEP cache
     download_cache             = false // DO NOT Download annotation cache
 
+    // Control Pileup QUAL options
+    ctrl_min_base_qual              = 13
+    ctrl_min_base_qual_contigs      = 1
+
     // Filter PE options
     basequal                   = 13
     mapqual                    = 30