Added bedtools sorted flag as default

@a.h.b.bollen: This is for you, can you test is this uses less memory then?

See merge request !395

Extract impute to vcf as separated pipeline



See merge request !413

fixed a config value



See merge request !417

Fix star mapping keep unmapped reads in bamfile

An addition of a config value to the `Mapping` pipeline. Let Star output unmapped reads.

See merge request !416

Fix mapping precentage

Fixes #349 

See merge request !412

Added autodetect fileformat paired

Fixed #350 

See merge request !414

Added more filter options

fixes #316 

See merge request !410

remove gatk-specific parts from license

Fixes #343 

@h.mei @p.j.van_t_hof Could you check this? Thanks :-). 

See merge request !406

Conflicts:
	bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

Fix mapping plot in report

Fixes #349 

See merge request !411

Somehow the rootpath was broken

fixes #347 

See merge request !408