In term of algorithms, what is the difference between haplotypecaller and unifiedgenotyper

bbsunchen · March 2016

Under every poster of GATK asking which is better, HC or UG, Geraldine always said HC.

So Is there any documents talking about the detail algorithms HC and UG are using, so that I can get a clear idea why HC is better?

Thanks.

Sheila · March 2016

@bbsunchen
Hi,

The HaplotypeCaller algorithm is documented in these four documents:
https://www.broadinstitute.org/gatk/guide/article?id=4147
https://www.broadinstitute.org/gatk/guide/article?id=4146
https://www.broadinstitute.org/gatk/guide/article?id=4441
https://www.broadinstitute.org/gatk/guide/article?id=4442

-Sheila

P.S. The major difference between HaplotypeCaller and UnifiedGenotyper is in the first 3 steps. The math for genotyping is the same between the two (last document).

In term of algorithms, what is the difference between haplotypecaller and unifiedgenotyper

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