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Old 10-17-2016, 04:46 AM   #1
swindhard
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Location: Germany

Join Date: Oct 2016
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Default 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
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Old 10-20-2016, 10:14 AM   #2
husamia
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You might try free VariantInterpreter from Illumina
https://variantinterpreter.informatics.illumina.com
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