Index

A

add_metadata() (VariantSet method) ADFilter (class in phe.variant_filters.ADFilter) annotate() (Annotator method) (CoverageAnnotator method) Annotator (class in phe.annotations)

available_annotators() (in module phe.annotations) available_callers() (in module phe.variant.variant_factory) available_filters() (in module phe.variant_filters) available_mappers() (in module phe.mapping.mapping_factory)

B

Bowtie2Mapper (class in phe.mapping.Bowtie2Mapper)

BWAMapper (class in phe.mapping.BWAMapper)

C

calculate_memory_for_sort() (in module phe.utils) call_concensus() (PHEFilterBase static method) CoverageAnnotator (class in phe.annotations.CoverageAnnotator)

create_aux_files() (Bowtie2Mapper method) (BWAMapper method) (GATKVariantCaller method) (MPileupVariantCaller method) (Mapper method) (VariantCaller method) customize_parser() (phe.variant_filters.ADFilter.ADFilter class method) (phe.variant_filters.DP4Filter.DP4Filter class method) (phe.variant_filters.DepthFilter.DepthFilter class method) (phe.variant_filters.GQFilter.GQFilter class method) (phe.variant_filters.GTFilter.UncallableGTFilter class method) (phe.variant_filters.MQ0FFilter.MQ0FFilter class method) (phe.variant_filters.MQ0Filter.MQ0Filter class method) (phe.variant_filters.MQFilter.MQFilter class method) (phe.variant_filters.QualFilter.QualFilter class method)

D

decode() (PHEFilterBase static method) decoder_pattern (PHEFilterBase attribute) DepthFilter (class in phe.variant_filters.DepthFilter) DP4Filter (class in phe.variant_filters.DP4Filter)

dynamic_annotator_loader() (in module phe.annotations) dynamic_caller_loader() (in module phe.variant.variant_factory) dynamic_filter_loader() (in module phe.variant_filters) dynamic_mapper_loader() (in module phe.mapping.mapping_factory)

F

factory() (in module phe.mapping.mapping_factory) (in module phe.variant.variant_factory) filter_name() (PHEFilterBase method)

filter_variants() (VariantSet method)

G

GATKVariantCaller (class in phe.variant.GATKVariantCaller) get_config() (PHEFilterBase method) get_info() (Bowtie2Mapper method) (BWAMapper method) (GATKVariantCaller method) (MPileupVariantCaller method) (Mapper method) (VariantCaller method) get_meta() (Annotator method) (Mapper method) (PHEMetaData method) (VariantCaller method) get_meta_values() (Annotator method) (CoverageAnnotator method)

get_records() (ParallelVCFReader method) get_samples() (ParallelVCFReader method) get_samtools_version() (Mapper method) get_version() (Bowtie2Mapper method) (BWAMapper method) (GATKVariantCaller method) (MPileupVariantCaller method) (Mapper method) (VariantCaller method) GQFilter (class in phe.variant_filters.GQFilter)

I

is_gap() (PHEFilterBase method) (UncallableGTFilter method) is_n() (PHEFilterBase method) (UncallableGTFilter method)

is_uncallable() (in module phe.utils.reader) (PHEFilterBase method)

M

magic_sep (PHEFilterBase attribute) make_annotators() (in module phe.annotations) make_bam() (Mapper method) make_filters() (in module phe.variant_filters) make_sam() (Bowtie2Mapper method) (BWAMapper method) (Mapper method) make_vcf() (GATKVariantCaller method) (MPileupVariantCaller method) (VariantCaller method)

Mapper (class in phe.mapping) MPileupVariantCaller (class in phe.variant.MPileupVariantCaller) MQ0FFilter (class in phe.variant_filters.MQ0FFilter) MQ0Filter (class in phe.variant_filters.MQ0Filter) MQFilter (class in phe.variant_filters.MQFilter)

N

name (ADFilter attribute) (Annotator attribute) (BWAMapper attribute) (Bowtie2Mapper attribute) (CoverageAnnotator attribute) (DP4Filter attribute) (DepthFilter attribute) (GATKVariantCaller attribute) (GQFilter attribute) (MPileupVariantCaller attribute) (MQ0FFilter attribute) (MQ0Filter attribute) (MQFilter attribute) (Mapper attribute) (QualFilter attribute) (UncallableGTFilter attribute)

P

ParallelVCFReader (class in phe.utils.reader) parameter (ADFilter attribute) (DP4Filter attribute) (DepthFilter attribute) (GQFilter attribute) (MQ0FFilter attribute) (MQ0Filter attribute) (MQFilter attribute) (PHEFilterBase attribute) (QualFilter attribute) (UncallableGTFilter attribute) phe (module) phe.annotations (module) phe.annotations.CoverageAnnotator (module) phe.mapping (module) phe.mapping.Bowtie2Mapper (module) phe.mapping.BWAMapper (module) phe.mapping.mapping_factory (module) phe.metadata (module) phe.utils (module) phe.utils.reader (module) phe.variant (module) phe.variant.GATKVariantCaller (module)

phe.variant.MPileupVariantCaller (module) phe.variant.variant_factory (module) phe.variant_filters (module) phe.variant_filters.ADFilter (module) phe.variant_filters.DepthFilter (module) phe.variant_filters.DP4Filter (module) phe.variant_filters.GQFilter (module) phe.variant_filters.GTFilter (module) phe.variant_filters.MQ0FFilter (module) phe.variant_filters.MQ0Filter (module) phe.variant_filters.MQFilter (module) phe.variant_filters.QualFilter (module) PHEFilterBase (class in phe.variant_filters) PHEMetaData (class in phe.metadata)

Q

QualFilter (class in phe.variant_filters.QualFilter)

S

short_desc() (ADFilter method) (DP4Filter method) (DepthFilter method) (GQFilter method) (MQ0FFilter method) (MQ0Filter method) (MQFilter method) (PHEFilterBase method) (QualFilter method) (UncallableGTFilter method)

str_to_filters() (in module phe.variant_filters)

U

UncallableGTFilter (class in phe.variant_filters.GTFilter)

update() (ParallelVCFReader method)

V

validate() (GATKVariantCaller method) (Mapper method) (VariantCaller method) VariantCaller (class in phe.variant) variants() (VariantSet method)

VariantSet (class in phe.variant) VCFTemplate (class in phe.variant)

W

write_variants() (VariantSet method)