Portion heritability explained BLINK output

[brian.phi...@gmail.com]

Hello Meng -

A quick question on BLINK - I have been experimenting with it recently, and so far it seems very stable and fast. However, I was wondering if it is possible to calculate the SNP r^2 value like GAPIT does. Everything that I run in BLINK I also run in GAPIT, so I am not sure if I could use the r^2 estimate generated by the CMLM, or if this would be incorrect.

Thank you,

Brian

[Meng Huang]

Hi Brian,

Unfortunately, BLINK only generate P value and MAF in the output result. But I think the other value like r^2 came from GAPIT could also be used in your report or paper. Thanks.

[Meng Huang]

Yes, we improved BioGPU and changed it’s name to BLINK. Thanks for your asking.

Meng

On Jul 5, 2016, at 11:14 AM, Brian Ward <brian.phi...@gmail.com> wrote:

Hi Meng -

Thank you for your reply. That makes sense. As far as I am aware, BLINK is not testing single markers at a time (correct me if I'm wrong), so I guess that would make the r^2 calculation impossible.

By the way, is BLINK a continuation of BioGPU?

Thank you again Meng.

Brian