genotype matrix
Entering edit mode
2.5 years ago

Hello. my university give me a zip file that contain VCF and its tbi So, I have one VCF file that contains many variants for many person. and tbi that I didn't open it until now.

I want to create a simple genotype matrix genotype matrix consists of row and columns of course which the row is define the person and the columns is ID of variants
then I fill row/column with the ref columns that related to it. All information I found it in VCF expect person.

So, from where can I extract the person info such as id so I know this info related to this id? and how???? also where can I use tbi file?

I'm using linux and python

Thank you very much

structure python • 629 views
Entering edit mode
2.5 years ago
desouzareis.r ▴ 280


I think you should start understanding the VCF format. In this document you will find helpful information. The file is compressed by bgzip tool and indexed by tabix which generates the .tbi file.


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