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compbiocore / VariantVisualization.jl

Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:
https://compbiocore.github.io/VariantVisualization.jl/stable/
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LoadError: KeyError: key "GT" not found #107

Open marciomagrini opened 3 years ago

marciomagrini commented 3 years ago

Hi guys,

I'm trying VIVA with .vcf file generated with MANTA software and I got this message:

Welcome to VIVA.

Loading dependency packages:

┌ Warning: ORCA.jl has been deprecated and all savefig functionality │ has been implemented directly in PlotlyBase itself. │ │ By implementing in PlotlyBase.jl, the savefig routines are automatically │ available to PlotlyJS.jl also. └ @ ORCA ~/.julia/packages/ORCA/U5XaN/src/ORCA.jl:8 ...

Finished loading packages!

Reading SJBALL030999.somaticSV.vcf ...

No filters applied. Large vcf files will take a long time to process and heatmap visualizations will lose resolution at this scale unless viewed in interactive html for zooming.

Loading VCF file into memory for visualization Selected 192 variants with no filters applied ERROR: LoadError: KeyError: key "GT" not found Stacktrace: [1] genotype(record::GeneticVariation.VCF.Record, indexes::UnitRange{Int64}, key::String) @ GeneticVariation.VCF ~/.julia/packages/GeneticVariation/r8DAL/src/vcf/record.jl:598 [2] generate_genotype_array(record_sub::Vector{Any}, y::String) @ VariantVisualization ~/.julia/packages/VariantVisualization/1yoNl/src/vcf_utils_complete.jl:668 [3] combined_all_genotype_array_functions(sub::Vector{Any}) @ VariantVisualization ~/.julia/packages/VariantVisualization/1yoNl/src/vcf_utils_complete.jl:617 [4] top-level scope @ /usr/local/bin/viva:409 in expression starting at

/usr/local/bin/viva:407

I've been reading the issues page but can't find anything related to this error. I'm using VIVA 1.6 in a MAC.

Any ideas?

Thank you!

gtollefson commented 2 years ago

Hi @marciomagrini,

I'm sorry for my delayed response. It looks like there's an aspect of the VCF file formatting that the GeneticVariation.jl VCF parser is not expecting. I would post this issue on the GeneticVariation.jl issues page and they will likely be able to sort out a fix with us.

If you're able, can you send me a screenshot or sample of a few complete lines of the VCF file you are using as well as the complete header? I can check out a few other possible sources of the error.

Thanks, George