Index

A

aaf (cyvcf2.cyvcf2.Variant attribute) add_filter_to_header() (cyvcf2.cyvcf2.VCF method) add_format_to_header() (cyvcf2.cyvcf2.VCF method)

add_info_to_header() (cyvcf2.cyvcf2.VCF method) add_to_header() (cyvcf2.cyvcf2.VCF method) ALT (cyvcf2.cyvcf2.Variant attribute)

C

call_rate (cyvcf2.cyvcf2.Variant attribute) CHROM (cyvcf2.cyvcf2.Variant attribute)

close() (cyvcf2.cyvcf2.Writer method) contains() (cyvcf2.cyvcf2.VCF method)

E

end (cyvcf2.cyvcf2.Variant attribute)

F

FILTER (cyvcf2.cyvcf2.Variant attribute) FILTERS (cyvcf2.cyvcf2.Variant attribute)

FORMAT (cyvcf2.cyvcf2.Variant attribute) format() (cyvcf2.cyvcf2.Variant method) from_string() (cyvcf2.cyvcf2.Writer method)

G

gen_variants() (cyvcf2.cyvcf2.VCF method) genotypes (cyvcf2.cyvcf2.Variant attribute) get_header_type() (cyvcf2.cyvcf2.VCF method) gt_alt_depths (cyvcf2.cyvcf2.Variant attribute) gt_alt_freqs (cyvcf2.cyvcf2.Variant attribute) gt_bases (cyvcf2.cyvcf2.Variant attribute) gt_depths (cyvcf2.cyvcf2.Variant attribute)

gt_phases (cyvcf2.cyvcf2.Variant attribute) gt_phred_ll_het (cyvcf2.cyvcf2.Variant attribute) gt_phred_ll_homalt (cyvcf2.cyvcf2.Variant attribute) gt_phred_ll_homref (cyvcf2.cyvcf2.Variant attribute) gt_quals (cyvcf2.cyvcf2.Variant attribute) gt_ref_depths (cyvcf2.cyvcf2.Variant attribute) gt_types (cyvcf2.cyvcf2.Variant attribute)

H

header_iter() (cyvcf2.cyvcf2.VCF method)

I

ID (cyvcf2.cyvcf2.Variant attribute) INFO (class in cyvcf2.cyvcf2) (cyvcf2.cyvcf2.Variant attribute) is_deletion (cyvcf2.cyvcf2.Variant attribute)

is_indel (cyvcf2.cyvcf2.Variant attribute) is_mnp (cyvcf2.cyvcf2.Variant attribute) is_snp (cyvcf2.cyvcf2.Variant attribute) is_sv (cyvcf2.cyvcf2.Variant attribute) is_transition (cyvcf2.cyvcf2.Variant attribute)

N

name (cyvcf2.cyvcf2.Writer attribute) num_called (cyvcf2.cyvcf2.Variant attribute) num_het (cyvcf2.cyvcf2.Variant attribute)

num_hom_alt (cyvcf2.cyvcf2.Variant attribute) num_hom_ref (cyvcf2.cyvcf2.Variant attribute) num_unknown (cyvcf2.cyvcf2.Variant attribute)

P

ploidy (cyvcf2.cyvcf2.Variant attribute)

POS (cyvcf2.cyvcf2.Variant attribute)

Q

QUAL (cyvcf2.cyvcf2.Variant attribute)

R

raw_header (cyvcf2.cyvcf2.VCF attribute)

REF (cyvcf2.cyvcf2.Variant attribute) relatedness() (cyvcf2.cyvcf2.VCF method)

S

samples (cyvcf2.cyvcf2.VCF attribute) seqlens (cyvcf2.cyvcf2.VCF attribute) seqnames (cyvcf2.cyvcf2.VCF attribute) set_format() (cyvcf2.cyvcf2.Variant method)

set_index() (cyvcf2.cyvcf2.VCF method) set_pos() (cyvcf2.cyvcf2.Variant method) set_samples() (cyvcf2.cyvcf2.VCF method) start (cyvcf2.cyvcf2.Variant attribute)

V

var_type (cyvcf2.cyvcf2.Variant attribute) Variant (class in cyvcf2.cyvcf2)

variant_from_string() (cyvcf2.cyvcf2.Writer method) VCF (class in cyvcf2.cyvcf2)

W

write_header() (cyvcf2.cyvcf2.Writer method)

write_record() (cyvcf2.cyvcf2.Writer method) Writer (class in cyvcf2.cyvcf2)