Skip to main content

Variant Call Format

Import a BCF/VCF file as PopData​

vcf(infile::String; rename_loci::Bool, silent::Bool, allow_monomorphic::Bool)
bcf(infile::String; rename_loci::Bool, silent::Bool, allow_monomorphic::Bool)

PopGen.jl provides the commands vcf and bcf to import a variant call format files into PopData. The reader also accepts files that are gzipped.

Arguments​

  • infile::String : path to file, in quotes. must end in .gz if gzipped

Keyword Arguments​

  • rename_loci::Bool: whether to simplify loci names to snp_# (default: false)
  • allow_monomorphic::Bool : whether to keep monomorphic loci (default: false)
  • silent::Bool : whether to print file information during import (default: false)

Example​

cabbage = bcf("/home/data/nappa_cabbage.bcf", rename_loci = true, silent = true)
potato = vcf("/home/data/russet_potatoes.vcf.gz", allow_monomorphic = true)

Mixed-Ploidy data​

In the event your variant call file is for mixed-ploidy data (where ploidy is not the same across all samples, e.g. PoolSeq), you will need to perform an additional step after reading in your data as PopData to convert the .genodata.genotype column into a GenoArray:

julia> mydata = bcf("path/to/file.bcf", silent = true, rename_loci = true) ;

julia> mydata.genodata.genotype =  mydata.genodata.genotype |> Array{Union{Missing, NTuple}}
WIP

The extra step required by mixed-ploidy data is a work in progress. Feel free to submit a PR if you have ideas!

Format​

Variant Call Format files follow a format standard, and while there is some wiggle-room for optional values, PopGen.jl only requires the core/mandatory components of a BCF/VCF, meaning problems should hopefully not arise regardless of which variant caller you are using (although we use Freebayes ourselves). Please open an issue if they do, or reach out to us on the community Slack.

Allele encodings​

When converting to PopData, the nucleotides will be recoded according to the table below. Note that this system differs slightly from how PGDSpider2 recodes alleles (the 3 and 4 are switched).

BaseATCG
Allele1234
VCF Filtering

Keep in mind, BCF/VCF files need to be filtered before importing them into PopGen.jl. There is no and will be no VCF-filtering functionality to this package, as it is outside of the purpose of PopGen.jl. Refer to vcftools, bcftools, and vcflib to filter your sequence data.

What BCF/VCF files contain​

Due to the nature of the file format, importing variant call files will provide:

  • sample names
  • ploidy of each sample
  • locus names
  • genotypes

What BCF/VCF files lack​

  • population information
  • geographical coordinate information

This means you will need to add that information separately afterwards. Location data (which is optional) can be added to the PopData with the locations! command. Population names (mandatory) can be added using populations!()

Acknowledgements​

The heavy lifting of the BCF/VCF reader is thanks to the tremendous efforts of the contributors involved with GeneticVariation.jl, and its successor VariantCallFormat.jl which we use to parse files into PopData format. More specifically, the two packages use a file parser created from Automa.jl. If you love the file importer, then give those folks your thanks. If something is wrong and/or you hate the importer, blame us first (and please open up an issue 😅).