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some genotype calls are wrong, why?

jimmikeselfjimmikeself Member
edited October 2012 in Ask the GATK team

Hello the team,

For some genotypes, it seems are wrong, I know it's model based, and base q, map q, etc are considered in the model.
I also read this link:
http://gatkforums.broadinstitute.org/discussion/1235/why-didnt-the-unified-genotyper-call-my-snp-i-can-see-it-right-there-in-igv#latest
But my case are special,
the format is (ref allele count)/(alternative allele count) genotype call:
22/24 0/0
109/125 0/0
85/109 0/0
26/32 0/0
40/161 0/0
195/6 1/1
239/5 1/1
83/6 1/1
46/28 1/1

In one case, the two variants are adjacent to each other.
In some case, they are one base indels.

Thanks,

Jim

Post edited by Geraldine_VdAuwera on

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