Go Back   SEQanswers > Applications Forums > Genomic Resequencing
View Poll Results: Which utility should convert a VCF file to Circos-ready files?
vcftools 1 12.50%
samtools ( 2 25.00%
circos 4 50.00%
a new/different project 4 50.00%
Multiple Choice Poll. Voters: 8. You may not vote on this poll

Similar Threads
Thread Thread Starter Forum Replies Last Post
Understanding VCF format ketan_bnf Bioinformatics 48 07-09-2014 08:24 PM
1000 genomes VCF format? yuanzhi Bioinformatics 14 02-26-2013 01:16 AM
conversion from CASAVA to VCF format kjaja Bioinformatics 0 12-08-2011 12:14 PM
VCF format from mileup Rachelly Bioinformatics 0 07-02-2011 11:54 PM
VCF format question NGS2009 Bioinformatics 1 02-14-2011 05:07 AM

Thread Tools
Old 01-20-2012, 12:33 PM   #1
Junior Member
Location: San Francisco, CA, USA

Join Date: Sep 2011
Posts: 1
Default VCF to Circos format(s)


Does anyone know if there is a utility out there ( from samtools? vcftools?) that can convert variants in a VCF file to a file that can be loaded into Circos for visualization? (e.g. highlights track)

Or has everybody just rolled their own and kept it private?


bzdyelnik is offline   Reply With Quote
Old 01-30-2012, 04:56 AM   #2
Location: Spain

Join Date: Jul 2010
Posts: 68

It would be definitely interesting to have a good
= interactive+graphical+platform-independent
visualizer for vcf files (also customized ones with extra fields).
sdvie is offline   Reply With Quote
Old 04-17-2012, 08:08 AM   #3
Location: washington DC

Join Date: Oct 2011
Posts: 21

Has anyone fold a solution to vcf files and circos?
apadr007 is offline   Reply With Quote
Old 05-18-2012, 12:05 PM   #4
Location: Gothenburg/Uppsala, Sweden

Join Date: Oct 2010
Posts: 82

Unless you want to do something really sophisticated it's often easy to parse things out with simple unix one-liners (cut, grep, awk etc.) and format them into the Circos formats.
gaffa is offline   Reply With Quote
Old 05-27-2014, 08:23 AM   #5
Senior Member
Location: USA

Join Date: Sep 2012
Posts: 130

This thread is now two years old, but still seems to be the most relevant hit on the subject. Is there still not a proper VCF to CIRCOS tool?
id0 is offline   Reply With Quote
Old 03-01-2022, 09:41 PM   #6
Junior Member
Location: India

Join Date: Mar 2022
Posts: 1

Apparently this thread is 10 years old now, yet no clear answer.
ambu is offline   Reply With Quote

circos, vcf, vcftools, vcfutils, visualization

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 07:18 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO