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Old 06-14-2011, 02:39 PM   #2
Location: Berkeley

Join Date: Feb 2011
Posts: 30

Are these matched normals or you have 16 individuals in all?

Running in all together would get you an average of everything, which would be a bad idea. Unless you think that your SNP of interest would be in all tumors, even putting these together would be inadvisable.

GATK specifically says to be REALLY careful about just running the genotyper and removing the SNPs in the normals. It might be ok if you're looking for a few interesting mutations that you can verify manually, but it's not ideal for large-scale efforts.

The authors of GATK say that they have their own effort underway, but it's not public yet. I know of another yet-unreleased effort but I don't know of of any publicly available genotyper for tumor-normal pairs.
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