MAF could be the REF clarification

francois-a / fastqtl

Enhanced version of the FastQTL QTL mapper

GNU General Public License v3.0

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MAF could be the REF clarification #16

Closed biostair closed 3 years ago

biostair commented 3 years ago

This will look the same clarification that I asked about via the tensorQTL [https://github.com/broadinstitute/tensorqtl/issues/38]!! But this time I came via the GTEX pipeline documentation page that mentions FastQTL being used.

To triple check, in FastQTL as well as tensorQTL, if the REF is not the major allele in certain cases, then it is reported as the MAF value.

Thanks (again)

francois-a commented 3 years ago

Hi, yes, thats correct. The output is exactly the same in FastQTL and tensorQTL.

biostair commented 3 years ago

I thought that would be the case. Thanks!