Merge pull request #13 from freerkvandijk/master

Fixed bug in imputation pipeline, added first version of phasing pipeline.
Test worksheet
Merge pull request #14 from PatrickDeelen/master

test worksheet impute2
Updated impute2 imputation step

Diverse improvements of bash scripts
Added some missing inputs
Default on repro back to PBS
Updated impute2 merge step

Fixed bash array handeling
Bug fix impute2
Merge pull request #15 from PatrickDeelen/master

Impute2 updates
Added impute2 file option
Update readme
Merge pull request #16 from PatrickDeelen/master

Impute2 update and readme update
bug fix in parameters
Merge pull request #17 from georgebyelas/master

Bug fix in parameters
First version imputation QC pipeline using ImputationTool.