VCF file with imputed data

[came203]

Dear team,

very useful method that I'm running already for genotyped data, but also wanted to run on VCF files containing imputed data.
When running the command (Julia 1.8.5):

ordinalgwas(@formula(trait ~ sex), datadir * "pheno.txt", gendir * "chr22",pvalfile="chr22"; geneticformat = "VCF", vcftype = :DS)

I get the following error message

ERROR: MethodError: no method matching isless(::Int64, ::Nothing)
Closest candidates are:
  isless(::Integer, ::ForwardDiff.Dual{Ty}) where Ty at ~/.julia/packages/ForwardDiff/QdStj/src/dual.jl:145
  isless(::Integer, ::Result) at ~/.julia/packages/NLopt/OIUOZ/src/NLopt.jl:81
  isless(::Real, ::Static.StaticInteger{Y}) where Y at ~/.julia/packages/Static/Ldb7F/src/Static.jl:456
  ...
Stacktrace:
  [1] <(x::Int64, y::Nothing)
    @ Base ./operators.jl:356
  [2] >(x::Nothing, y::Int64)
    @ Base ./operators.jl:382
  [3] copy_ds!(A::Vector{Union{Missing, Float64}}, reader::VariantCallFormat.Reader; key::String, model::Symbol, impute::Bool, center::Bool, scale::Bool, msg::String, sampleID::Nothing, record_chr::Vector{Any}, record_pos::Vector{Any}, record_ids::Vector{Any}, record_ref::Nothing, record_alt::Nothing)
    @ VCFTools ~/.julia/packages/VCFTools/qtvvr/src/convert.jl:702
  [4] WARNING: both OrdinalMultinomialModels and Distributions export "cor"; uses of it in module OrdinalGWAS must be qualified
WARNING: both OrdinalMultinomialModels and Distributions export "loglikelihood"; uses of it in module OrdinalGWAS must be qualified
(::OrdinalGWAS.var"#26#32"{FormulaTerm{ContinuousTerm{Float64}, Term}, Symbol, Symbol, UnitRange{Int64}, NLopt.Optimizer, StatsModels.TableRegressionModel{OrdinalMultinomialModel{Int64, Float64, LogitLink}, Matrix{Float64}}, Symbol, Bool, DataFrame, VariantCallFormat.Reader})(io::IOStream)
    @ OrdinalGWAS ~/.julia/packages/OrdinalGWAS/azVl0/src/gwas.jl:724
  [5] makestream(::OrdinalGWAS.var"#26#32"{FormulaTerm{ContinuousTerm{Float64}, Term}, Symbol, Symbol, UnitRange{Int64}, NLopt.Optimizer, StatsModels.TableRegressionModel{OrdinalMultinomialModel{Int64, Float64, LogitLink}, Matrix{Float64}}, Symbol, Bool, DataFrame, VariantCallFormat.Reader}, ::String, ::Vararg{String})       
    @ SnpArrays ~/.julia/packages/SnpArrays/60wqu/src/codec.jl:31
  [6] ordinalgwas(fittednullmodel::StatsModels.TableRegressionModel{OrdinalMultinomialModel{Int64, Float64, LogitLink}, Matrix{Float64}}, vcffile::String, nsamples::Int64, vcftype::Symbol; analysistype::String, testformula::FormulaTerm{ContinuousTerm{Float64}, Term}, test::Symbol, pvalfile::String, snpmodel::Val{1}, snpinds::
Nothing, vcfrowinds::UnitRange{Int64}, solver::NLopt.Optimizer, solver_config::Dict{String, Any}, verbose::Bool, snpset::Nothing, e::Nothing)
    @ OrdinalGWAS ~/.julia/packages/OrdinalGWAS/azVl0/src/gwas.jl:695
  [7] ordinalgwas(fittednullmodel::StatsModels.TableRegressionModel{OrdinalMultinomialModel{Int64, Float64, LogitLink}, Matrix{Float64}}, geneticfile::String; analysistype::String, geneticformat::String, vcftype::Symbol, testformula::FormulaTerm{ContinuousTerm{Float64}, Term}, test::Symbol, pvalfile::String, snpmodel::Val{1},
 snpinds::Nothing, geneticrowinds::Nothing, solver::NLopt.Optimizer, solver_config::Dict{String, Any}, verbose::Bool, snpset::Nothing, e::Nothing)
    @ OrdinalGWAS ~/.julia/packages/OrdinalGWAS/azVl0/src/gwas.jl:228
  [8] ordinalgwas(nullformula::FormulaTerm{Term, NTuple{12, Term}}, nulldf::DataFrame, geneticfile::String; nullfile::String, link::LogitLink, solver::NLopt.Optimizer, solver_config::Dict{String, Any}, verbose::Bool, kwargs::Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol, Symbol}, NamedTuple{(:pvalfile, :geneticformat, :vcftype
), Tuple{String, String, Symbol}}})
    @ OrdinalGWAS ~/.julia/packages/OrdinalGWAS/azVl0/src/gwas.jl:134
  [9] ordinalgwas(nullformula::FormulaTerm{Term, NTuple{12, Term}}, covfile::String, geneticfile::String; covtype::Nothing, covrowinds::Nothing, kwargs::Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol, Symbol}, NamedTuple{(:pvalfile, :geneticformat, :vcftype), Tuple{String, String, Symbol}}})
    @ OrdinalGWAS ~/.julia/packages/OrdinalGWAS/azVl0/src/gwas.jl:112
 [10] top-level scope
    @ REPL[11]:1

The VCF file was constructed coming from a BGEN file:

plink2 --bgen chr22.bgen ref-first --sample chr22.sample --export vcf bgz vcf-dosage=DS --minimac3-r2-filter 0.5 --out chr22

Going directly to the BGEN file doesn't work, as I don't seem to be able to find the option on how to integrate the .sample file with the .bgen file in OrdinalGWAS

[kose-y]

First, we have been missing the support for .sample files with the BGEN files, and it is now added. I'm tagging a new version, v0.6.3, which will be available in the registry in about 15-30 minutes.

For the VCF file, the error message seems like the DS field is missing for at least one SNP. Please check if you have the DS key in your file correctly. If only some SNPs are without the DS key, we have a bug dealing with the missing DS key in the VCFTools package. I think it can be fixed soon. @biona001

[kose-y]

The syntax for .sample file is:

ordinalgwas(@formula(y ~ sex), datadir * "bgen_ex.csv", 
    datadir * "bgen_test"; geneticformat = "BGEN", samplepath="bgen-sample-file.sample")