GATK UnifiedGenotyper
Hi there,
for my analyses I'm using a panel of human individuals from the SGDP which have been called with UnifiedGenotyper.
Since I have reanalyzed this data with a different approach (e.g. reference, aligner, and caller), I was wondering what is the exact model used by UnifiedGenotyper as it would help me to understand the difference between the two approaches.
I couldn't find much other than that is based on Bayesian genotype likelihood, but nothing specific on the exact information is using in the INFO field... the simple description in the header doesn't help me understand whether all those details contribute to the actual number of SNPs and INDELs called.
Let me know, thanks in advance!
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There are 2 sources that you can check for our old documentation. The below article explains majority of the algorithms in concise format.
https://www.nature.com/articles/ng.806
Since UnifiedGenotyper is a very old tool the best writing on that is available under GATK2 docs.
Most hyperlinks won't work now but wayback machine can get you most of them successfully.
I hope these would help.
Regards.
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Gökalp Çelik thanks, much appreciated! I see the documentation is quite rich for SNP type events, a bit less for INDELs but overall conveys the necessary information given the tool is quite outdated — as you pointed out.
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