Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: How to convert VarScan TAB format to VCF?
1
gravatar for SmallChess
3.8 years ago by
SmallChess • 500
Australia
SmallChess • 500 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 COMMENT • link •
modified 11 months ago by marcofraca • 10 • written 3.8 years ago by SmallChess • 500

germline calling of tumor-normal paired sample germline by varscan2

ADD REPLY • link written 14 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 14 months ago by ATpoint ♦ 29k
1
gravatar for marcofraca
11 months 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 11 months ago • written 11 months ago by marcofraca • 10
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1085 users visited in the last hour