Added qsub script skeleton for bwa exome pipeline from Javed's group.
Updated with sickle and bwa steps.
Changed sampe to also do sorting/BAM conversion (via pipes)
Updated.
Added cleansam step.
Added cleansam step to job list.
Fixed typo in indexbam1 (reading params from yaml config)
Added flagstat step.
Finished cleansam step.
Added merge_bam step
Added bwa helpers.
Added picard markdups. Changed it to use java from command line
instead of python wrapper.
Updated markdups runner.
Updated docstring for markdups runner.
Updated param passing method, and added GATK steps.
Updated more cmd line module loads.
Removed second indexing and added CREATE_INDEX param to picard steps.
Fixed typo in run mark dups (param dict name).
Fixed issue with format of input files; changed from using python
wrapper to java cmd line, need INPUT=filename for each input file.
Updated.