INIFILE	settings/base.ini

PRESTATS	yes
MAPPING	yes
POSTSTATS	yes
INDELREALIGNMENT	yes
BASEQUALITYRECAL	no
VARIANT_CALLING	yes
FILTER_VARIANTS	yes
SOMATIC_VARIANTS	yes
COPY_NUMBER	yes
BAF	no
ANNOTATE_VARIANTS	yes
KINSHIP	yes
FINALIZE	yes

INIFILE	settings/base.ini

PRESTATS	yes
MAPPING	yes
POSTSTATS	yes
INDELREALIGNMENT	no
BASEQUALITYRECAL	yes
VARIANT_CALLING	yes
FILTER_VARIANTS	yes
SOMATIC_VARIANTS	yes
COPY_NUMBER	yes
BAF	no
ANNOTATE_VARIANTS	yes
KINSHIP	yes
FINALIZE	yes

Enable BQSR in favour of realignment
Enable BQSR in favour of realignment
