Bayesian genotyper

mehar

Hi,

Could anyone say how the GATK bayesian genotyper is different from samtools bayesian genotyper? Also, could some one provide a source for the mathematical notes of the GATK and samtools bayesian genotypers?

Geraldine_VdAuwera

Hi there,

Regarding the UnifiedGenotyper, the mathematical notes are available in the publication:

DePristo M, Banks E, Poplin R, Garimella K, Maguire J, Hartl C, Philippakis A, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell T, Kernytsky A, Sivachenko A, Cibulskis K, Gabriel S, Altshuler D and Daly, M (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics. 43:491-498.

And additional material is given in this article:

http://gatkforums.broadinstitute.org/discussion/1237

Regarding the samtools genotyper, you'll need to contact the authors directly.

Geraldine_VdAuwera

Hi there,

Regarding the UnifiedGenotyper, the mathematical notes are available in the publication:

DePristo M, Banks E, Poplin R, Garimella K, Maguire J, Hartl C, Philippakis A, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell T, Kernytsky A, Sivachenko A, Cibulskis K, Gabriel S, Altshuler D and Daly, M (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics. 43:491-498.

And additional material is given in this article:

http://gatkforums.broadinstitute.org/discussion/1237

Regarding the samtools genotyper, you'll need to contact the authors directly.

mehar

Geraldine_VdAuwera

@Geraldine_VdAuwera said:

Hi there,

Regarding the UnifiedGenotyper, the mathematical notes are available in the publication:

Regarding the samtools genotyper, you'll need to contact the authors directly.

Thanks.

Would you give some suggestions to fix the plots issue using baserecalibrator which i have posted earlier?