How to convert VarScan TAB format to VCF?

Question

[scchess]

I have some VarScan generated TAB format files (default format) that I want to convert into VCF for IGV visuzaliation. I don't have the source files to regenerate by VarScan again (VarScan has an option for VCF but I don't input files).

Any script that can do that?

[eric_li]

germline calling of tumor-normal paired sample germline by varscan2

[ATpoint]

As this does not answer the question on how to convert tab2vcf, I moved it to a comment.

Answer 1

[marcofraca]

Hi, Some years have passed but maybe someone is still interested in it. Here there is a python script that should do the job:

If it doesn't work you can try this one:

https://github.com/student-t/Varscan2VCF