API

vcf.Reader

class vcf.Reader(fsock=None, filename=None, compressed=None, prepend_chr=False, strict_whitespace=False, encoding='ascii')[source]

Reader for a VCF v 4.0 file, an iterator returning _Record objects

alts = None

ALT fields from header

contigs = None

contig fields from header

fetch(chrom, start=None, end=None)[source]

Fetches records from a tabix-indexed VCF file and returns an iterable of _Record instances

chrom must be specified.

The start and end coordinates are in the zero-based, half-open coordinate system, similar to _Record.start and _Record.end. The very first base of a chromosome is index 0, and the the region includes bases up to, but not including the base at the end coordinate. For example fetch('4', 10, 20) would include all variants overlapping a 10 base pair region from the 11th base of through the 20th base (which is at index 19) of chromosome 4. It would not include the 21st base (at index 20). See http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms for more information on the zero-based, half-open coordinate system.

If end is omitted, all variants from start until the end of the chromosome chrom will be included.

If start and end are omitted, all variants on chrom will be returned.

requires pysam

filters = None

FILTER fields from header

formats = None

FORMAT fields from header

infos = None

INFO fields from header

metadata = None

metadata fields from header (string or hash, depending)

next()[source]

Return the next record in the file.

vcf.Writer

class vcf.Writer(stream, template, lineterminator='n')[source]

VCF Writer. On Windows Python 2, open stream with ‘wb’.

close()[source]

Close the writer

flush()[source]

Flush the writer

write_record(record)[source]

write a record to the file

vcf.model._Record

class vcf.model._Record(CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, sample_indexes, samples=None)[source]

A set of calls at a site. Equivalent to a row in a VCF file.

The standard VCF fields CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO and FORMAT are available as properties.

The list of genotype calls is in the samples property.

Regarding the coordinates associated with each instance:

  • POS, per VCF specification, is the one-based index (the first base of the contig has an index of 1) of the first base of the REF sequence.
  • The start and end denote the coordinates of the entire REF sequence in the zero-based, half-open coordinate system (see http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms), where the first base of the contig has an index of 0, and the interval runs up to, but does not include, the base at the end index. This indexing scheme is analagous to Python slice notation.
  • The affected_start and affected_end coordinates are also in the zero-based, half-open coordinate system. These coordinates indicate the precise region of the reference genome actually affected by the events denoted in ALT (i.e., the minimum affected_start and maximum affected_end).
    • For SNPs and structural variants, the affected region includes all bases of REF, including the first base (i.e., affected_start = start = POS - 1).
    • For deletions, the region includes all bases of REF except the first base, which flanks upstream the actual deletion event, per VCF specification.
    • For insertions, the affected_start and affected_end coordinates represent a 0 bp-length region between the two flanking bases (i.e., affected_start = affected_end). This is analagous to Python slice notation (see http://stackoverflow.com/a/2947881/38140). Neither the upstream nor downstream flanking bases are included in the region.
POS = None

the one-based coordinate of the first nucleotide in REF

aaf

A list of allele frequencies of alternate alleles. NOTE: Denominator calc’ed from _called_ genotypes.

affected_end = None

zero-based, half-open end coordinate of affected region of reference genome (not included in the region)

affected_start = None

zero-based, half-open start coordinate of affected region of reference genome

alleles = None

list of alleles. [0] = REF, [1:] = ALTS

call_rate

The fraction of genotypes that were actually called.

end = None

zero-based, half-open end coordinate of REF

genotype(name)[source]

Lookup a _Call for the sample given in name

get_hets()[source]

The list of het genotypes

get_hom_alts()[source]

The list of hom alt genotypes

get_hom_refs()[source]

The list of hom ref genotypes

get_unknowns()[source]

The list of unknown genotypes

heterozygosity

Heterozygosity of a site. Heterozygosity gives the probability that two randomly chosen chromosomes from the population have different alleles, giving a measure of the degree of polymorphism in a population.

If there are i alleles with frequency p_i, H=1-sum_i(p_i^2)

is_deletion

Return whether or not the INDEL is a deletion

is_filtered

Return True if a variant has been filtered

is_indel

Return whether or not the variant is an INDEL

is_monomorphic

Return True for reference calls

is_snp

Return whether or not the variant is a SNP

is_sv

Return whether or not the variant is a structural variant

is_sv_precise

Return whether the SV cordinates are mapped to 1 b.p. resolution.

is_transition

Return whether or not the SNP is a transition

nucl_diversity

pi_hat (estimation of nucleotide diversity) for the site. This metric can be summed across multiple sites to compute regional nucleotide diversity estimates. For example, pi_hat for all variants in a given gene.

Derived from: “Population Genetics: A Concise Guide, 2nd ed., p.45” John Gillespie.

num_called

The number of called samples

num_het

The number of heterozygous genotypes

num_hom_alt

The number of homozygous for alt allele genotypes

num_hom_ref

The number of homozygous for ref allele genotypes

num_unknown

The number of unknown genotypes

samples = None

list of _Calls for each sample ordered as in source VCF

start = None

zero-based, half-open start coordinate of REF

sv_end

Return the end position for the SV

var_subtype

Return the subtype of variant.

  • For SNPs and INDELs, yeild one of: [ts, tv, ins, del]

  • For SVs yield either “complex” or the SV type defined in the ALT fields (removing the brackets). E.g.:

    <DEL>       -> DEL
    <INS:ME:L1> -> INS:ME:L1
    <DUP>       -> DUP
    

The logic is meant to follow the rules outlined in the following paragraph at:

http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

“For precisely known variants, the REF and ALT fields should contain the full sequences for the alleles, following the usual VCF conventions. For imprecise variants, the REF field may contain a single base and the ALT fields should contain symbolic alleles (e.g. <ID>), described in more detail below. Imprecise variants should also be marked by the presence of an IMPRECISE flag in the INFO field.”

var_type

Return the type of variant [snp, indel, unknown] TO DO: support SVs

vcf.model._Call

class vcf.model._Call(site, sample, data)[source]

A genotype call, a cell entry in a VCF file

data

Namedtuple of data from the VCF file

gt_bases

The actual genotype alleles. E.g. if VCF genotype is 0/1, return A/G

gt_type

The type of genotype. hom_ref = 0 het = 1 hom_alt = 2 (we don;t track _which+ ALT) uncalled = None

is_filtered

Return True for filtered calls

is_het

Return True for heterozygous calls

is_variant

Return True if not a reference call

phased

A boolean indicating whether or not the genotype is phased for this sample

sample

The sample name

site

The _Record for this _Call

vcf.model._AltRecord

class vcf.model._AltRecord(type, **kwargs)[source]

An alternative allele record: either replacement string, SV placeholder, or breakend

type = None

String to describe the type of variant, by default “SNV” or “MNV”, but can be extended to any of the types described in the ALT lines of the header (e.g. “DUP”, “DEL”, “INS”...)

vcf.model._Substitution

class vcf.model._Substitution(nucleotides, **kwargs)[source]

A basic ALT record, where a REF sequence is replaced by an ALT sequence

sequence = None

Alternate sequence

vcf.model._SV

class vcf.model._SV(type, **kwargs)[source]

An SV placeholder

vcf.model._SingleBreakend

class vcf.model._SingleBreakend(orientation, connectingSequence, **kwargs)[source]

A single breakend

vcf.model._Breakend

class vcf.parser._Breakend(chr, pos, orientation, remoteOrientation, connectingSequence, withinMainAssembly, **kwargs)[source]

A breakend which is paired to a remote location on or off the genome

connectingSequence = None

The breakpoint’s connecting sequence.

orientation = None

The orientation of breakend. If the sequence 3’ of the breakend is connected, True, else if the sequence 5’ of the breakend is connected, False.

remoteOrientation = None

The orientation of breakend’s mate. If the sequence 3’ of the breakend’s mate is connected, True, else if the sequence 5’ of the breakend’s mate is connected, False.

withinMainAssembly = None

If the breakend mate is within the assembly, True, else False if the breakend mate is on a contig in an ancillary assembly file.