some genotype calls are wrong, why?

jimmikeselfjimmikeself Posts: 10Member
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: 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.



Post edited by Geraldine_VdAuwera on


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