iss17 batch for gatk setup
iss17 checkin to move to burnet
updates to bowtie2
Merge branch 'master' of github.com:BauerLab/ngsane
iss17_GATKsplit: final version run through smokebox
Merge branch 'iss17_GATKsplit'
iss17_GATKsplit add sample configs
bugfix pindel, variant collect and update of gatk_DOC; added the option for resultfilename in prepare jobsubmission
Merge branch 'master' of github.com:BauerLab/ngsane
trigger DBROD var renamed to DBSNPVCF; smokebox for pindel
Merge branch 'master' of github.com:BauerLab/ngsane
update to smokebox, bugfix bigwig, bugfix pindel
bugfix in pindel_config
Merge remote-tracking branch 'upstream/master' into filedetection

Conflicts:
	core/prepareJobSubmission.sh
	mods/bowtie2.sh
	smokebox/makefile
	smokebox/result/expected/SummaryCHIPSEQ.html
	smokebox/result/expected/SummaryTOPHATCUFFHTSEQ.html
	smokebox/result/expected/SummaryVARCALLS.html