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Question: How to convert VarScan TAB format to VCF?
1
gravatar for SmallChess
3.0 years ago by
SmallChess • 480
Australia
SmallChess • 480 wrote:

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?
varscan2 genome • 1.4k views
ADD COMMENT • link •
modified 6 weeks ago by marcofraca • 10 • written 3.0 years ago by SmallChess • 480

germline calling of tumor-normal paired sample germline by varscan2

ADD REPLY • link written 4 months ago by eric_li • 0

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

ADD REPLY • link written 4 months ago by ATpoint ♦ 15k
1
gravatar for marcofraca
6 weeks ago by
marcofraca • 10
marcofraca • 10 wrote:

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 modified 6 weeks ago • written 6 weeks ago by marcofraca • 10
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