Merge remote-tracking branch 'remotes/origin/develop' into feature-qiime

...in/scala/org/example/group/pipelines/BiopetPipeline.scala

protected/biopet-gatk-extensions/pom.xml

...umc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala

...c/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala

...mc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala

.../sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala

.../sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala

...a/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala

...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

...sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala

.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

...main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala

...lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala

...iopet/pipelines/gatk/variantcallers/HaplotypeCaller.scala

...pipelines/gatk/variantcallers/HaplotypeCallerAllele.scala

...t/pipelines/gatk/variantcallers/HaplotypeCallerGvcf.scala

...opet/pipelines/gatk/variantcallers/UnifiedGenotyper.scala

...ipelines/gatk/variantcallers/UnifiedGenotyperAllele.scala

.../sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala

...c/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp