INIFILE	settings/include/hmf_settings.ini

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

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

SOMATIC_VARIANTS	yes

COPY_NUMBER	no

AMBER	yes
COBALT	yes
PURPLE	yes
BAF	no

SV_CALLING	yes
SV_MODE	sample_control
SV_MANTA	yes
SV_DELLY	no

KINSHIP	no
GENDER	no

HEALTHCHECK	yes
FINALIZE	yes
INIFILE	settings/include/hmf_settings.ini

PRESTATS	yes
MAPPING	yes
POSTSTATS	yes
EXONCALLCOV	no
CALLABLE_LOCI	no
DAMAGE_ESTIMATE	yes
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	yes

COPY_NUMBER	no

AMBER	yes
COBALT	yes
PURPLE	yes
BAF	no

SV_CALLING	yes
SV_MODE	sample_control
SV_MANTA	yes
SV_DELLY	no

KINSHIP	no
GENDER	no

HEALTHCHECK	yes
FINALIZE	yes
Switch germline calling back on in somatic pipeline
Switch germline calling back on in somatic pipeline
