INIFILE	settings/include/hmf_settings.ini

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

VARIANT_CALLING	no
FILTER_VARIANTS	no
ANNOTATE_VARIANTS	no

SOMATIC_VARIANTS	yes
SOMVAR_ANNOTATE	yes
SOMVAR_STRELKA	yes
SOMVAR_VARSCAN	yes
SOMVAR_FREEBAYES	yes
SOMVAR_MUTECT	yes

STRELKA_PATH	/data/tools/strelka_v1.0.14
STRELKA_INI	strelka_config_bwa_genome.ini

COPY_NUMBER	no

SV_CALLING	no

BAF	no
CALLABLE_LOCI	no
KINSHIP	yes
GENDER	no
FINALIZE	yes

INIFILE	settings/include/hmf_settings.ini

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

VARIANT_CALLING	no
FILTER_VARIANTS	no
ANNOTATE_VARIANTS	no

SOMATIC_VARIANTS	yes
SOMVAR_ANNOTATE	yes
SOMVAR_STRELKA	yes
SOMVAR_VARSCAN	yes
SOMVAR_FREEBAYES	yes
SOMVAR_MUTECT	yes

STRELKA_PATH	/data/tools/strelka_v1.0.14
STRELKA_INI	strelka_config_bwa_genome.ini

COPY_NUMBER	no

SV_CALLING	no

BAF	no
CALLABLE_LOCI	no
KINSHIP	no
GENDER	no
FINALIZE	yes

Switch off kinship - cant run kinship without germline calling
Switch off kinship - cant run kinship without germline calling
