Merge branch 'develop' into BIOWDL-282

CHANGELOG.md

@@ -12,6 +12,7 @@ that users understand how the changes affect the new version.
 version 1.0.0-dev
 ---------------------------
 + GATK: SplitNCigarReads, BaseRecalibration and ApplyBQSR do no longer need regions files as required inputs.
++ VarDict: Add user definable flags (-M, -A, -Q, -d, -v, -f) to the paired VCF filtering script.
 + Cutadapt: If the output is a gzipped file, compress with level 1 (instead of default 6).
 + Cutadapt: Fix issues with read2output when using single-end reads.
 + Add feature type, idattr and additional attributes to htseq-count.

vardict.wdl

@@ -20,6 +20,13 @@ task VarDict {
         Int endColumn = 3
         Int geneColumn = 4
 
+        Boolean outputCandidateSomaticOnly = true
+        Boolean outputAllVariantsAtSamePosition = true
+        Float mappingQuality = 20
+        Int minimumTotalDepth = 8
+        Int minimumVariantDepth = 4
+        Float minimumAlleleFrequency = 0.02
+
         Int threads = 1
         Int memory = 16
         Float memoryMultiplier = 2.5
@@ -45,6 +52,12 @@ task VarDict {
         ~{true="var2vcf_paired.pl" false="var2vcf_valid.pl" defined(normalBam)} \
         -N "~{tumorSampleName}~{"|" + normalSampleName}" \
         ~{true="" false="-E" defined(normalBam)} \
+        ~{true="-M" false="" outputCandidateSomaticOnly} \
+        ~{true="-A" false="" outputAllVariantsAtSamePosition} \
+        -Q ~{mappingQuality} \
+        -d ~{minimumTotalDepth} \
+        -v ~{minimumVariantDepth} \
+        -f ~{minimumAlleleFrequency} \
         > ~{outputVcf}
     }