class Bio::DB::Vcf

Extends the methods of the Bio::DB::Vcf class in bio-samtools. A Vcf object represents the VCF format described at www.1000genomes.org/node/101 . The Bio::DB::Vcf object returns all information in the VCF line, but the implementation here acts as if there is only possibly one variant at each position and ignores positions at which there may be multiple variants. Vcf format is only used when the Bio::Util::Gngm object requests information about indels using SAMtools mpileup method.

Public Instance Methods

alternatives() click to toggle source

List of alternate alleles at this locus, obtained by splitting the vcf.alt attribute string on commas

Example vcf.alt = “ACT,TCA”

vcf.alternatives = ["ACT", "TCA"]

vcf.alt = “T”

vcf.alternatives = ["T"]

# File lib/bio/util/bio-gngm.rb, line 123
def alternatives
  self.alt.split(",") rescue []
end

gq() click to toggle source

Returns the genotype quality score from the sample data (as defined by the Vcf GQ attribute) for the first sample in the Vcf only.

# File lib/bio/util/bio-gngm.rb, line 146
def gq 
  self.samples["1"]["GQ"].to_f rescue 0.0
end

is_indel?(options) click to toggle source

Returns true if ref col is different in length from any of the entries in alt column

# File lib/bio/util/bio-gngm.rb, line 186
def is_indel?(options)
  return true if self.variant? and self.alternatives.any? {|x| x.length != self.ref.length} and self.pass_quality?(options)
  false
end

is_mnp?(options) click to toggle source

returns true if ref col has same length as all alternatives and position variant passes quality

# File lib/bio/util/bio-gngm.rb, line 174
def is_mnp?(options)
  return true if self.alternatives.all? {|x| x.length == self.ref.length} and self.pass_quality?(options)
  false
end

is_snp?(options) click to toggle source

returns true if ref col has length of 1 and is_mnp?

# File lib/bio/util/bio-gngm.rb, line 180
def is_snp?(options)
  return true if self.is_mnp?(options) and self.ref.length == 1
  false
end

mq() click to toggle source

Returns the mean Mapping Quality from the reads over this position as defined by the Vcf MQ attribute.

# File lib/bio/util/bio-gngm.rb, line 141
def mq
  self.info["MQ"].to_f rescue 0.0
end

non_ref_allele_count() click to toggle source

Returns the depth of reads containing the non reference allele. IE the sum of the last two figures in the DP4 attribute.

# File lib/bio/util/bio-gngm.rb, line 128
def non_ref_allele_count
  self.info["DP4"].split(",")[2..3].inject {|sum,n| sum.to_f + n.to_f } rescue 0.0
end

non_ref_allele_freq() click to toggle source

Returns the non-reference allele frequency based on depth of reads used for the genotype call,

vcf.non_ref_allele_count / vcf.used_depth

# File lib/bio/util/bio-gngm.rb, line 136
def non_ref_allele_freq
  self.non_ref_allele_count / self.used_depth
end

pass_quality?(options) click to toggle source

Returns true if the position passes criteria

Options and Defaults:

:min_depth => 2
:min_non_ref_count => 2
:mapping_quality => 10

Example

vcf.pass_quality?(:min_depth => 5, :min_non_ref_count => 2, :mapping_quality => 25, :min_snp_quality => 20)

# File lib/bio/util/bio-gngm.rb, line 169
def pass_quality?(options)
  (self.used_depth >= options[:min_depth] and self.mq >= options[:mapping_quality] and self.non_ref_allele_count >= options[:min_non_ref_count] and self.qual >= options[:min_snp_quality])
end

pl() click to toggle source

Returns the phred scaled likelihood of the first non-reference allele (as defined by the Vcf PL attribute) for the first sample in the Vcf only.

# File lib/bio/util/bio-gngm.rb, line 151
def pl
  self.samples["1"]["PL"].split(",")[1].to_f rescue 0.0
end

to_s() click to toggle source

Return a short string representing chromosome, position, reference sequence, alt sequence(s) and the info string of the Vcf object.

# File lib/bio/util/bio-gngm.rb, line 107
def to_s
  "#{self.chrom} #{self.pos} #{self.ref} #{self.alt} #{self.info}"
end

used_depth() click to toggle source

The depth of reads actually used in the genotype call by Vcftools. The sum of the DP4 attribute. Returns 0.0 if no value is calculated.

# File lib/bio/util/bio-gngm.rb, line 112
def used_depth
  self.info["DP4"].split(",").inject {|sum,n| sum.to_f + n.to_f} rescue 0.0
end

variant?() click to toggle source

returns true if the alt column of the Vcf is not .

Examples

vcf record = 20 14370 rs6054257 G A 29 PASS …

vcf.variant? #=> true

vcf record = 20 1230237 . T . 47 PASS …

vcf.variant? #=> false

# File lib/bio/util/bio-gngm.rb, line 102
def variant?
  not self.alt == "." rescue false
end