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	yes
SOMVAR_ANNOTATE	yes
SOMVAR_STRELKA	yes

COPY_NUMBER	yes
CNV_MODE	sample_control
CNV_FREEC	yes
FREEC_BAF	yes
CNV_QDNASEQ	no

SV_CALLING	yes
SV_MODE	sample_control
SV_MANTA	yes
SV_DELLY	no

BAF	no
CALLABLE_LOCI	no
KINSHIP	yes
GENDER	no
PURPLE	yes
DAMAGE_ESTIMATE	yes
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	yes
SOMVAR_ANNOTATE	yes
SOMVAR_STRELKA	yes

COPY_NUMBER	yes
CNV_MODE	sample_control
CNV_FREEC	yes
FREEC_BAF	yes
CNV_QDNASEQ	no

SV_CALLING	yes
SV_MODE	sample_control
SV_MANTA	yes
SV_DELLY	no

BAF	no
CALLABLE_LOCI	no
KINSHIP	yes
GENDER	no
PURPLE	no
DAMAGE_ESTIMATE	yes
FINALIZE	yes

Switch off purple in somatic ini
Switch off purple in somatic ini
