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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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bcftools and incorrect genotypes - still an issue? #427

Open cfriedline opened 8 years ago

cfriedline commented 8 years ago

Hi - wanted to revisit this and see if it's still a problem with recent versions of bcftools. Quickly scanning my data, it does not appear to be, but wanted to get confirmation.

From @lh3 on https://www.biostars.org/p/12354/:

Yes, this is a flaw of bcftools and that is exactly why bcftools does not output genotypes by default.

On the other hand, the whole idea of bcftools is to do inference without knowing genotypes. Bcftools never looks at the genotypes itself infers, but can pretty accurately estimate site allele frequency, compute the LD r^2, discovery very rare mutations and test association and HWE. Actually if you ascertain genotypes without imputation and then do things above, you frequently get much worse results.

So, my suggestion is not to look at genotypes. Bcftools has already computed many statistics you are interested in, only in the right way.

lh3 commented 8 years ago

That comment was made 4.6 years ago. A lot have happened after that. My comment that time is not necessarily applicable to the latest bcftools.

cfriedline commented 8 years ago

Thanks @lh3 - I'm aware of the time, but haven't been able to find any direct answer searching more recent threads. Are the genotypes reported by bcftools trustworthy in recent versions?