Bug fix in VCF to table protocol
fixed conflict in merge
Merge branch 'master' of https://github.com/molgenis/molgenis-pipelines
fixing aborted pull
Merge pull request #37 from pneerincx/master

Improved demultiplex protocol
Merge branch 'master' of https://github.com/molgenis/molgenis-pipelines
Included DataTransfer.sh.ftl in standard NGS_alignment pipeline.
Merge pull request #38 from freerkvandijk/master

Added dataTransfer protocol
Update on MergeIndelCalls protocol. Sorting of VCF file now done in separate perl script.
Merge pull request #39 from freerkvandijk/master

Update on mergeIndelCalls protocol
Added automatic detection of number of mismatches between all barcodes per lane, for determening demulitplexng with 1 or 0 possible mismatches
Merge pull request #40 from Gerbenvandervries/master

Added automatic detection of number of mismatches between all barcode for Illumina demultiplexing
NGS concordance one sample against all check.
Merge pull request #41 from freerkvandijk/master

Quick concordance check pipeline
missing [sample_index] on line 47 in CreateInhouseProjects.ftl for SR demultiplexedSampleFastqChecksumFilenameSR inserted
Merge pull request #42 from ljohansson/master

added missing [sample_index]  at demultiplexedSampleFastqChecksumFilenameSR in CreateInhouseProjects.ftl