Implemented covariate table calculation.
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.
VariantCalling implemented. Since HaplotypeCaller can't run on multiple cores, parallelism done by execution per chromosome.
Merge pull request #98 from freerkvandijk/master

In-house pipeline upto variant calling
Merge branch 'master' of https://github.com/molgenis/molgenis-pipelines