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bcm-uga / pcadapt

Performing highly efficient genome scans for local adaptation with R package pcadapt v4
https://bcm-uga.github.io/pcadapt
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SNPs thinning LD clumping #67

Closed msalamon2 closed 2 years ago

msalamon2 commented 3 years ago

Hi,

I am applying pcadapt to a dataset of pool-seq whole genome sequencing for 12 populations (~50 million SNPs). I tried to apply SNPs thinning with the LD.clumping option, but I get the same number of SNPs with or without thinning (and identical results for loadings plot, screeplot etc). I tried with different window size and r2 threshold but it's always the same number of SNPs before and after thinning. Based on the results from another analysis, I am almost certain that there is LD in my dataset. Could this be because this option is not supported for pool-seq data ?

Thank you

privefl commented 3 years ago

Yes, I don't think this is supported. You can't really infer LD with 12 population averages.