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View Poll Results: Which utility should convert a VCF file to Circos-ready files?
vcftools 1 12.50%
samtools (vcfutils.pl) 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

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Old 01-20-2012, 12:33 PM   #1
bzdyelnik
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Location: San Francisco, CA, USA

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Default VCF to Circos format(s)

Hi,

Does anyone know if there is a utility out there (vcfutils.pl 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?

Thanks,

Jesse
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Old 01-30-2012, 04:56 AM   #2
sdvie
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It would be definitely interesting to have a good
= interactive+graphical+platform-independent
visualizer for vcf files (also customized ones with extra fields).
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Old 04-17-2012, 08:08 AM   #3
apadr007
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Has anyone fold a solution to vcf files and circos?
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Old 05-18-2012, 12:05 PM   #4
gaffa
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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.
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Old 05-27-2014, 08:23 AM   #5
id0
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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?
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