MINOR cleanup and bugfixes
CONFIG gatk variant calling
BUGFIX in primerUsage stats
MINOR bugfixes
CHANGED source bam/sam for custom metrics (capture amplicon stats before chimeras are filtered)
BUGFIX haplotypeCaller task fix
BUGFIX haplotypeCaller parameters
BUGFIX haplotypeCaller parameters (that was a biggie actually)
BUGFIX haplotypeCaller parameters (that was a biggie actually v2)
DEACTIVATED haplotypeCaller
DEACTIVATED monomorphic calling for FB
MINOR
FIXED collectCustomMetrics was overwriting alignment file
ENABLED haplotypecaller
REWROTE parsePicard
BUGFIX
BUGFIX
CONFIG change
FIXED primerBED in ampliconFilter
ADDED lockfile and implemented safer writing for Filemanager JSON file
CONFIG change