Question: How to convert VarScan TAB format to VCF?
1
gravatar for SmallChess
3.0 years ago by
SmallChess480
Australia
SmallChess480 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 COMMENTlink modified 6 weeks ago by marcofraca10 • written 3.0 years ago by SmallChess480

germline calling of tumor-normal paired sample germline by varscan2

ADD REPLYlink written 4 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 4 months ago by ATpoint15k
1
gravatar for marcofraca
6 weeks 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 6 weeks ago • written 6 weeks ago by marcofraca10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1664 users visited in the last hour