Question: How to convert VarScan TAB format to VCF?
1
gravatar for SmallChess
3.8 years ago by
SmallChess500
Australia
SmallChess500 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 • 1.9k views
ADD COMMENTlink modified 11 months ago by marcofraca10 • written 3.8 years ago by SmallChess500

germline calling of tumor-normal paired sample germline by varscan2

ADD REPLYlink written 14 months ago by eric_li0

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

ADD REPLYlink written 14 months ago by ATpoint29k
1
gravatar for marcofraca
11 months ago by
marcofraca10
marcofraca10 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 COMMENTlink modified 11 months ago • written 11 months ago by marcofraca10
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