INIFILE	settings/include/hmf_settings.ini

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

VARIANT_CALLING	no
CALLING_GVCF	no
FILTER_VARIANTS	no
ANNOTATE_VARIANTS	no

SOMATIC_VARIANTS	yes
SOMVAR_STRELKA	yes
SOMVAR_ANNOTATE	yes

COPY_NUMBER	yes
AMBER	no
COBALT	yes
PURPLE	no
CNV_MODE	sample_control
CNV_FREEC	no
FREEC_BAF	no
BAF	no
CNV_QDNASEQ	no

SV_CALLING	yes
SV_MODE	sample_control
SV_MANTA	yes
SV_DELLY	no

KINSHIP	no
GENDER	no

FINALIZE	yes
HEALTHCHECK	yes

INIFILE	settings/include/hmf_settings.ini

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

VARIANT_CALLING	no
CALLING_GVCF	no
FILTER_VARIANTS	no
ANNOTATE_VARIANTS	no

SOMATIC_VARIANTS	yes
SOMVAR_STRELKA	yes
SOMVAR_ANNOTATE	yes

COPY_NUMBER	yes
AMBER	yes
COBALT	yes
PURPLE	yes
CNV_MODE	sample_control
CNV_FREEC	no
FREEC_BAF	no
BAF	no
CNV_QDNASEQ	no

SV_CALLING	yes
SV_MODE	sample_control
SV_MANTA	yes
SV_DELLY	no

KINSHIP	no
GENDER	no

FINALIZE	yes
HEALTHCHECK	yes

Enable amber and purple for rerun
Enable amber and purple for rerun
