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-   -   Combining VCF from different callers (http://seqanswers.com/forums/showthread.php?t=72049)

swindhard 10-17-2016 04:46 AM

Combining VCF from different callers
 
Hi,

I'm searching for a tool to combine VCF files from different caller.

Since several paper now stated, what I've also measured, that the concordance of the different variant callers aren't too good, I would like to run the calling on multiple variant caller, and in the end combine the different calls. But I don't just want to combine them but instead get a VCF file containing all found variants an for each variant an entry in the INFO field how many of the caller found the mutation. In the end I want to filter on that criteria.

Now my question is, is do you know of any tool out there which does something like this? So far I couldn't find any. What I found was BAYSIC which does something similar, but already performes some kind of analysis.



Thanks in advance,
Swindhard

husamia 10-20-2016 10:14 AM

You might try free VariantInterpreter from Illumina
https://variantinterpreter.informatics.illumina.com


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