updates to bowtie2
Merge branch 'master' of github.com:BauerLab/ngsane
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