Index

_

_AltRecord (class in vcf.model) _Breakend (class in vcf.parser) _Call (class in vcf.model) _Record (class in vcf.model)

_SingleBreakend (class in vcf.model) _Substitution (class in vcf.model) _SV (class in vcf.model)

A

aaf (vcf.model._Record attribute) alleles (vcf.model._Record attribute)

alts (vcf.Reader attribute) AvgDepthPerSample (class in vcf.filters)

B

Base (class in vcf.filters)

C

call_rate (vcf.model._Record attribute) called (vcf.model._Call attribute) chr (vcf.parser._Breakend attribute)

close() (vcf.Writer method) connectingSequence (vcf.parser._Breakend attribute) customize_parser() (vcf.filters.Base class method)

D

data (vcf.model._Call attribute)

DepthPerSample (class in vcf.filters)

E

end (vcf.model._Record attribute)

ErrorBiasFilter (class in vcf.filters)

F

fetch() (vcf.Reader method) filter_name() (vcf.filters.Base method) filters (vcf.Reader attribute)

flush() (vcf.Writer method) formats (vcf.Reader attribute)

G

genotype() (vcf.model._Record method) get_hets() (vcf.model._Record method) get_hom_alts() (vcf.model._Record method) get_hom_refs() (vcf.model._Record method)

get_unknowns() (vcf.model._Record method) gt_alleles (vcf.model._Call attribute) gt_bases (vcf.model._Call attribute) gt_type (vcf.model._Call attribute)

I

infos (vcf.Reader attribute) is_deletion (vcf.model._Record attribute) is_het (vcf.model._Call attribute) is_indel (vcf.model._Record attribute) is_monomorphic (vcf.model._Record attribute)

is_snp (vcf.model._Record attribute) is_sv (vcf.model._Record attribute) is_sv_precise (vcf.model._Record attribute) is_transition (vcf.model._Record attribute) is_variant (vcf.model._Call attribute)

M

metadata (vcf.Reader attribute)

N

name (vcf.filters.Base attribute) next() (vcf.Reader method) nucl_diversity (vcf.model._Record attribute) num_called (vcf.model._Record attribute)

num_het (vcf.model._Record attribute) num_hom_alt (vcf.model._Record attribute) num_hom_ref (vcf.model._Record attribute) num_unknown (vcf.model._Record attribute)

O

orientation (vcf.parser._Breakend attribute)

P

phased (vcf.model._Call attribute)

pos (vcf.parser._Breakend attribute)

R

Reader (class in vcf)

remoteOrientation (vcf.parser._Breakend attribute)

S

sample (vcf.model._Call attribute) samples (vcf.model._Record attribute) sequence (vcf.model._Substitution attribute) site (vcf.model._Call attribute)

SiteQuality (class in vcf.filters) SnpOnly (class in vcf.filters) start (vcf.model._Record attribute) sv_end (vcf.model._Record attribute)

T

trim_common_suffix() (in module vcf.utils)

type (vcf.model._AltRecord attribute)

V

var_subtype (vcf.model._Record attribute) var_type (vcf.model._Record attribute) VariantGenotypeQuality (class in vcf.filters)

vcf (module) vcf.utils (module)

W

walk_together() (in module vcf.utils) withinMainAssembly (vcf.parser._Breakend attribute)

write_record() (vcf.Writer method) Writer (class in vcf)