Merge branch 'develop' into tooltests

docs/general/requirements.md

mkdocs.yml

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

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

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

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

...rces/nl/lumc/sasc/biopet/extensions/rscript/plotScatter.R

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala

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

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

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala

...nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala

.../nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala

.../scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala

.../main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala

...in/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala

.../src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala

...k/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala

.../main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala