VariantCall.jl

PopGenCore.jl/src/io/VariantCall.jl

📦 not exported	🟪 exported by PopGenCore.jl	🔵 exported by PopGen.jl

📦 openvcf

openvcf(::String)

Open VCF file (.vcf(.gz) or .bcf(.gz)) and return an IO stream in reading mode "r".

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🟪 bcf

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

Load a BCF file into memory as a PopData object. Population information needs to be provided separately.

• infile : path to BCF file (can be gzipped)

Keyword Arguments

• rename_loci : true/false of whether to simplify loci names to "snp_#" (default: false)
• allow_monomorphic : true/false of whether to keep monomorphic loci (default: false)
• silent: true/false of whether to print extra file information (default: false). Alleles are recoded according to the following schema:

Base	A	T	C	G
Allele	1	2	3	4

Mixed-ploidy data

If importing mixed-ploidy data (such as poolseq), you will need to perform an additional step to convert the genotype column into the correct GenoArray type:

julia> mydata = bcf("path/to/file.bcf", silent = true, rename_loci = true) ;
julia> mydata.genodata.genotype =  mydata.genodata.genotype |> Array{Union{Missing, NTuple}}

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🟪 vcf

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

Load a VCF file into memory as a PopData object. Population information needs to be provided separately.

• infile : path to VCF file (can be gzipped)

Keyword Arguments

• rename_loci : true/false of whether to simplify loci names to "snp_#" (default: false)
• allow_monomorphic : true/false of whether to keep monomorphic loci (default: false)
• silent: true/false of whether to print extra file information (default: false). Alleles are recoded according to the following schema:

Base	A	T	C	G
Allele	1	2	3	4

Mixed-ploidy data

If importing mixed-ploidy data (such as poolseq), you will need to perform an additional step to convert the genotype column into the correct GenoArray type:

julia> mydata = vcf("path/to/file.vcf", silent = true, rename_loci = true) ;
julia> mydata.genodata.genotype =  mydata.genodata.genotype |> Array{Union{Missing, NTuple}}