indel handling on vcfs
set a fixed version number for stability for GATK and Picard [ci skip]
also make tmpdir [ci skip]
fix variable name [ci skip]
add indelrealigner step prior to gatk [ci skip]
remove some code and move some others
demultiplexing steps
more info in hash [ci skip]
os.listdir [ci skip]
os.path.join [ci skip]
make_barcodes function call [ci skip]
util.files.read_tabfile function call [ci skip]
add an l to library id [ci skip]
fix variables and update recipe [ci skip]
var name fix
fix picardoptions
read structure [ci skip]
Picard wants the subdirectory, not the base Bustard directory [ci skip]
fix args, pull in read_structure [ci skip]
improve read group id hashing, fix date format for picard [ci skip]