Add flags to varDict filtering script "var2vcf_paired.pl"

Flag description:
  -M  If set, output only candidate somatic
  -A  Indicate to output all variants at the same position.  By default, only the variant with the highest allele frequency is converted to VCF
  -Q  float The minimum mapping quality.  Defaults to 0 for Illumina sequencing => Using -Q 20 as default
  -d  integer The minimum total depth.  Defaults to 5 => Using -d 8 as default
  -v  integer The minimum variant depth.  Defaults to 3 => Using -v 4 as default
  -f  float The minimum allele frequency.  Defaults to 0.02

Note that "-M" is a soft filter (see https://github.com/AstraZeneca-NGS/VarDictJava/issues/247). This means that there will still be variants with "STATUS=Germline" with a "PASS" filter.

vardict.wdl

@@ -20,6 +20,11 @@ task VarDict {
         Int endColumn = 3
         Int geneColumn = 4
 
+        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 +50,12 @@ task VarDict {
         ~{true="var2vcf_paired.pl" false="var2vcf_valid.pl" defined(normalBam)} \
         -N "~{tumorSampleName}~{"|" + normalSampleName}" \
         ~{true="" false="-E" defined(normalBam)} \
+        -M \
+        -A \
+        -Q ~{mappingQuality} \
+        -d ~{minimumTotalDepth} \
+        -v ~{minimumVariantDepth} \
+        -f ~{minimumAlleleFrequency} \
         > ~{outputVcf}
     }