Merge branch 'develop' of git.lumc.nl:biopet/biopet into feature-gears

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

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

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

.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala

...scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala

...ore/src/main/scala/nl/lumc/sasc/biopet/core/Version.scala

...src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala

...in/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala

...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala

.../lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala

...nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala

...umc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala

...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala

...l/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala

...a/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala

public/biopet-tools/src/test/resources/VEP_oneline.vcf

public/biopet-tools/src/test/resources/VEP_oneline.vcf.gz

...ic/biopet-tools/src/test/resources/VEP_oneline.vcf.gz.tbi

public/biopet-tools/src/test/resources/chrQ.vcf