Question

How to convert VarScan TAB format to VCF?

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8.6 years ago

scchess ▴ 640

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 • 5.0k views

ADD COMMENT • link updated 5.7 years ago by marcofraca ▴ 20 • written 8.6 years ago by scchess ▴ 640

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germline calling of tumor-normal paired sample germline by varscan2

ADD REPLY • link 6.0 years ago by eric_li • 0

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

ADD REPLY • link 6.0 years ago by ATpoint 85k

score 2 · Answer 1 · 2019-03-06

2

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5.7 years ago

marcofraca ▴ 20

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

ADD COMMENT • link 5.7 years ago by marcofraca ▴ 20