Cosmic vcf

[RockChalkJayhawk]

Does anyone have a VCF formatted file for the COSMIC database, or do I need to spend some time to write one?

[mra]

I'm looking for a tool to do the conversion (COSMIC to VCF). Did you come up with any?

[Bukowski]

I suspect that this is going to be one of those 'everyone rolls their own' situation. I really wish they would just release COSMIC in VCF format..

[RockChalkJayhawk]

In a developmental tool by GATK, one of the input files is a cosmic vcf see here https://confluence.broadinstitute.or...GATools/MuTect. I just emailed the group to find out where to download this file. I'll post if I here anything back.

[Bukowski]

Yes I'm aware that exists, but I'm not sure I can use it within the terms of the licence agreement for MuTect access

[Jon_Keats]

We generated a conversion script to so I could use GATK annotator to mark cosmic positions in a VCF. I can post the file on my site (http://www.keatslab.org/resources/ngs-tools/ngs-scripts). You are free to use it. It works in my hands though I didn't line by line verify that no mutations were skipped.

[RockChalkJayhawk]

Thanks John. Do you know if it uses only the positional information for annotation or the position combined with the type/alternate of variant?

[Bukowski]

We generated a conversion script to so I could use GATK annotator to mark cosmic positions in a VCF. I can post the file on my site (www.keatslab.org). You are free to use it. It works in my hands though I didn't line by line verify that no mutations were skipped.

That would be quite awesome Jon - thanks!

[Jon_Keats]

It's up at the update link now. For GATK annotator is only use the position information not coding changes. In my pipeline we annotate the VCF then use SNPeff to call coding changes. No sense annotating the coding changes when SNPeff redoes it each time in 1-2 minutes

[shyam_la]

It's up at the update link now. For GATK annotator is only use the position information not coding changes. In my pipeline we annotate the VCF then use SNPeff to call coding changes. No sense annotating the coding changes when SNPeff redoes it each time in 1-2 minutes

Hi Jon,

Can you upload v59 COSMIC in .vcf format?
Or how to go about making one, if I have the cosmic mutant export file from sanger..
I am a biologist and "rolling my own" won't be too easy..

Thank you.

Shyam.