This gem provides a lightweight class, Vcf, which can be used to parse VCF files by giving it one VCF line at a time.
To install, just install the vcf gem:
sudo gem install vcf
To print the DP (read depth) value of each entry, you might do this:
require 'vcf'
for line in gets
next if line[0] == "#" # Skip header if it exists
puts Vcf.new(line).info["DP"]
end
You can do something similar with a one-liner at the command line
cat test.vcf | ruby -r vcf -ne 'next if $_[0] == "#"; puts Vcf.new($_).info["DP"]'
You can also use the parse_line method to reuse the same Vcf object
require 'vcf'
v = Vcf.new
for line in gets
if v.parse_line(line) # Returns false if line starts with # (a header line)
puts v.info["DP"]
end
end
The Vcf class has the following member variables:
chrom: A string such as "chr1".pos: An integer, 1-based start position of the locus.id: A string, the name/id of the locus.ref: A string, the reference allele.alt: A string, the alternate allele.qual: An integer or a string ("."), the quality of the locus.filter: A string, the list of filters that the locus failed.info: A hash, describing the locus with string keys pointing to string values. For example vcf.info["DP"] == "20".format: A string or nil, the name of properties for all samples at this locus (nil if no samples are specified).samples: A hash, {sample name => {property_name => property_value}}. For example vcf.samples["sally"]["GT"] == "0/1". If sample_names were not specified when parsing the line, sample names in this hash will be "1", "2", ... etc. Top level hash is emtpy if no samples are specified.