INIFILE	settings/include/kg_settings.ini

PRESTATS	yes
MAPPING	yes
POSTSTATS	yes
EXONCALLCOV	no
INDELREALIGNMENT	yes
BASEQUALITYRECAL	no

VARIANT_CALLING	yes
CALLING_GVCF	yes
FILTER_VARIANTS	yes
ANNOTATE_VARIANTS	yes
ANNOTATE_SNPEFF	yes
ANNOTATE_SNPSIFT	yes
ANNOTATE_FREQUENCIES	yes
ANNOTATE_IDFIELD	yes
SOMATIC_VARIANTS	no

COPY_NUMBER	yes
CNV_MODE	sample
CNV_FREEC	yes
CNV_QDNASEQ	no

BAF	no
KINSHIP	no
FINALIZE	yes

INIFILE	settings/include/hmf_settings.ini

PRESTATS	yes
MAPPING	yes
POSTSTATS	yes
EXONCALLCOV	no
INDELREALIGNMENT	yes
BASEQUALITYRECAL	no

VARIANT_CALLING	yes
CALLING_GVCF	yes
FILTER_VARIANTS	yes
ANNOTATE_VARIANTS	yes
ANNOTATE_SNPEFF	yes
ANNOTATE_SNPSIFT	yes
ANNOTATE_FREQUENCIES	yes
ANNOTATE_IDFIELD	yes
SOMATIC_VARIANTS	no

COPY_NUMBER	yes
CNV_MODE	sample
CNV_FREEC	yes
CNV_QDNASEQ	no

BAF	no
KINSHIP	no
FINALIZE	yes

Switch single sample to inherit from hmf base settings
Switch single sample to inherit from hmf base settings
