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How to convert VarScan TAB format to VCF?

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?

genome varscan2
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updated by marcofraca • marcofraca • written by scchess scchess

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

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written by ATpoint ATpoint

1 answer

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

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written by marcofraca • marcofraca

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