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DReichLab / EIG

Eigen tools by Nick Patterson and Alkes Price lab
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Can smartpca output fst value for each SNP? #99

Closed minglibio closed 10 months ago

minglibio commented 10 months ago

Hi,

When I run smartpca to estimate the Hudson's fst, I only get a whole genome pair-wise fst. I am curious if I can get the fst value of each SNP using smartpca, if so, which parameter should I add?

The output I got is like this:

## Fst statistics between populations:     fst     fstjack       std error      Z    snpnumber
F_st                    pop1                    pop2    -0.004134750    -0.004133115     0.001098870    -3.761 241609

Best, Ming

bumblenick commented 10 months ago

fstdetailsname: fstsnpout: YES

bumblenick commented 10 months ago

fstdetailsname: fstsnpout: YES