Creating SNV matrix from VCF

[coh-racng]

The tutorial for Creating SNV matrix from VCF file is missing the commands for the final step as there is nothing after the following sentence:

Once the index generated, the matrices can be genereated easily:

Does that step involve using extract_matrices_from_dataset.py?

Where does one find cell barcode information in the VCF output from the SNV_calling pipeline? Perhaps I am missing something but I cannot find in the code the how you linked cell barcode to SNVs to generate the (cells x SNVs) matrix.

Update:
I realized that ExtractMatrix in extract_matrices_from_dataset.py specifies that the vcf folders are structured as one folder per single cell. So I am guessing that is why you are not accessing cell barcode in the VCF -> SNV matrix conversion?