to merge
public rna seq
Small bugfix in BwaAlign.sh, added readgroup line to cmd.
Made a start with CollectBamMetrics.sh protocol
Small bugfixes Lifelines genotypedata pipeline. Updates on new in-house NGS pipeline.
Fully functioning pipeline incl. picard metrics.
Implemented target realignment in in-house pipeline.
added additional params in phasing
Merge pull request #96 from freerkvandijk/master

Implemented new protocols in-house NGS pipeline
coutput liftover is bed,bim,fam
Implemented covariate table calculation.
fixed bug in merging imp chunks
fix bug in merge samples
corrected bug with arithmetic ops
Merge branch 'master' of https://github.com/molgenis/molgenis-pipelines
Merge pull request #97 from kantale/master

See comments
Functioning in-house pipeline upto VariantCalling
Merge branch 'master' of https://github.com/molgenis/molgenis-pipelines
Small updates to improve performance of 3 protocols.
genotype_harmonizer 1.1.1 -> 1.3.1