Increased time allocation for larger files. Added logging.
Minor changes to usage
Added extra error logging for multiple readgroups.
Major change - removal of function to run Local realignment split across chromosomes
Added GetTargetFile function
Increased time slightly for larger files
Added annotations to joint calling command
Added new target files: one for RefSeq intervals, the other is the union of RefSeq and all the capture kits
Update the hpc workarounds for the new cluster
Comments regarding modified annovar script for cadd phred scores
First draft, basically functional
First draft, basically functional
Updates to README
Removal of unwanted files