Merge remote-tracking branch 'origin/develop' into feature-external_examples

docs/tools/SamplesTsvToJson.md

protected/biopet-gatk-extensions/pom.xml

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

...asc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

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

...lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala

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

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

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

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

...l/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala

...biopet/extensions/gatk/broad/RealignerTargetCreator.scala

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

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

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

.../lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala

...sc/biopet/extensions/gatk/broad/VariantRecalibrator.scala

protected/biopet-gatk-pipelines/pom.xml

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

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