Error when using the jupyter notebook

[venkatk89]

Hello!,

I am trying to use the Jupyter notebook provided in the following link: https://github.com/compbiocore/VariantVisualization.jl/blob/master/VIVA.ipynb

I did the following changes for my analysis:

1) I changed the Jupyter kernel to Julia 1.8.5.

2) Gave the absolute path to my vcf file in the vcf_filename variable in Code block 1

I am using the phase 3 1000 genomes project vcf file for chr21. It can be obtained from here

3) Kept the default parameters for all other variables

4) When encountering errors in code block 6, installed the dependencies via julia in command line. The following commands were used:

• import Pkg; Pkg.add("ArgParse")
• Pkg.add("VariantVisualization")
• Pkg.add("GeneticVariation")

I am encountering an error at the final code block 7. The following is the error:

GeneticVariation.VCF.Reader file format error on line 1

Stacktrace:
 [1] error(::String, ::Int64)
   @ Base ./error.jl:44
 [2] _readheader!(reader::GeneticVariation.VCF.Reader, state::BioCore.Ragel.State{BufferedStreams.BufferedInputStream{IOStream}})
   @ GeneticVariation.VCF ~/.julia/packages/BioCore/YBJvb/src/ReaderHelper.jl:106
 [3] readheader!(reader::GeneticVariation.VCF.Reader)
   @ GeneticVariation.VCF ~/.julia/packages/BioCore/YBJvb/src/ReaderHelper.jl:80
 [4] Reader
   @ ~/.julia/packages/GeneticVariation/r8DAL/src/vcf/reader.jl:15 [inlined]
 [5] Reader
   @ ~/.julia/packages/GeneticVariation/r8DAL/src/vcf/reader.jl:28 [inlined]
 [6] jupyter_main(vcf_filename::String, saving_options::NTuple{5, String}, variant_filters::Tuple{String, String, String}, sample_selection::Tuple{String, String}, plotting_options::NTuple{4, String})
   @ VariantVisualization ~/.julia/packages/VariantVisualization/1yoNl/src/new_notebook_utils.jl:27
 [7] top-level scope
   @ In[14]:1

Am I doing something wrong here? Is this issue related to issue #100? Or is this error arising due to incompatibility of the VCF file and GeneticVariation.jl?

Thanks in advance!

P.S: If the codes for downloading missing dependencies are added to the notebook, it'll be easier for new users. If possible, kindly update them in your future releases.