Reader(fsock=None, filename=None, compressed=None, prepend_chr=False, strict_whitespace=False, encoding='ascii')¶
Reader for a VCF v 4.0 file, an iterator returning
ALT fields from header
contig fields from header
fetch(chrom, start=None, end=None)¶
Fetches records from a tabix-indexed VCF file and returns an iterable of
chrom must be specified.
The start and end coordinates are in the zero-based, half-open coordinate system, similar to
_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.
FILTER fields from header
FORMAT fields from header
INFO fields from header
metadata fields from header (string or hash, depending)
Return the next record in the file.
_Record(CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, sample_indexes, samples=None)¶
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
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
enddenote the coordinates of the entire
REFsequence 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
endindex. This indexing scheme is analagous to Python slice notation.
affected_endcoordinates 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
- 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
REFexcept the first base, which flanks upstream the actual deletion event, per VCF specification.
- For insertions, the
affected_endcoordinates represent a 0 bp-length region between the two flanking bases (i.e.,
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.
- For SNPs and structural variants, the affected region includes all bases of
the one-based coordinate of the first nucleotide in
A list of allele frequencies of alternate alleles. NOTE: Denominator calc’ed from _called_ genotypes.
zero-based, half-open end coordinate of affected region of reference genome (not included in the region)
zero-based, half-open start coordinate of affected region of reference genome
list of alleles.  = REF, [1:] = ALTS
The fraction of genotypes that were actually called.
zero-based, half-open end coordinate of
_Callfor the sample given in
The list of het genotypes
The list of hom alt genotypes
The list of hom ref genotypes
The list of unknown genotypes
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)
Return whether or not the INDEL is a deletion
Return True if a variant has been filtered
Return whether or not the variant is an INDEL
Return True for reference calls
Return whether or not the variant is a SNP
Return whether or not the variant is a structural variant
Return whether the SV cordinates are mapped to 1 b.p. resolution.
Return whether or not the SNP is a transition
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.
The number of called samples
The number of heterozygous genotypes
The number of homozygous for alt allele genotypes
The number of homozygous for ref allele genotypes
The number of unknown genotypes
_Callsfor each sample ordered as in source VCF
zero-based, half-open start coordinate of
Return the end position for the SV
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:
“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.”
Return the type of variant [snp, indel, unknown] TO DO: support SVs
_Call(site, sample, data)¶
A genotype call, a cell entry in a VCF file
Namedtuple of data from the VCF file
The actual genotype alleles. E.g. if VCF genotype is 0/1, return A/G
The type of genotype. hom_ref = 0 het = 1 hom_alt = 2 (we don;t track _which+ ALT) uncalled = None
Return True for filtered calls
Return True for heterozygous calls
Return True if not a reference call
A boolean indicating whether or not the genotype is phased for this sample
The sample name
An alternative allele record: either replacement string, SV placeholder, or breakend
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”...)
_SingleBreakend(orientation, connectingSequence, **kwargs)¶
A single breakend
_Breakend(chr, pos, orientation, remoteOrientation, connectingSequence, withinMainAssembly, **kwargs)¶
A breakend which is paired to a remote location on or off the genome
The breakpoint’s connecting sequence.
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.
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.
If the breakend mate is within the assembly, True, else False if the breakend mate is on a contig in an ancillary assembly file.