Allele frequency data can use in pcadapt?

[HengLiang1993]

Hi I am trying to use allele frequency to run the pcadapt.

I have a 180 samples from 18 population, and I want to check the outlier by the allele frequency in 18 population. I do not kown if I use the allele frequency to replace the allele count (like lfmm file) as input file in pcadapt is ok? my allele frequeny data is as this:

POS Population1 Population2 Population3 Population4 Population5 Population6 Population7 Population8 Population9 Population10 Population11 Population12 Population13 2_8711_G 0 0 0 0 0.166667 0 0 0 0 0 0 0 0 2_8722_C 0 0 0 0 0 0 0.05 0 0.05 0 0 0 0 2_8726_T 0.357143 0 0.0555556 0 0 0 0 0 0 0 0 0 0 2_8736_A 0 0.142857 0 0.222222 0 0 0 0 0 0 0 0 0 2_8742_T 0.1 0.0714286 0 0 0 0.111111 0 0.0833333 0 0 0 0 0.222222 2_8748_T 0 0 0 0 0.25 0 0 0 0 0 0 0 0 2_8754_A 0 0 0 0 0 0 0 0 0 0 0 0 0 2_8765_A 0 0 0 0 0 0.0625 0.05 0 0.05 0.0714286 0 0.0625 0 2_8773_T 0 0 0 0 0 0.125 0 0 0 0 0 0 0 2_8776_T 0 0 0 0 0 0 0 0 0 0 0 0 0 2_8778_T 0 0 0 0 0.25 0.0625 0.05 0 0.05 0 0 0.125 0 2_8779_T 0.125 0 0.0555556 0 0 0 0 0 0 0 0.277778 0 0.222222 2_8780_T 0.1 0 0 0 0 0 0.05 0 0.05 0 0 0.3125 0 2_8784_T 0 0 0 0 0.1 0.0555556 0.05 0 0.05 0 0.166667 0 0

Best

Heng

[privefl]

Have you looked at https://bcm-uga.github.io/pcadapt/articles/pcadapt.html#g--detecting-local-adaptation-with-pooled-sequencing-data?

[HengLiang1993]

Hi Yes, but my sequence is capture-Seq data, not the Pool-Seq data, and can it also apply？

[privefl]

I have no idea what that is, sorry. Is this a matrix of allele frequencies for many variants across multiple populations? If so, I think that's basically the same.

[HengLiang1993]

It is the matrix of allele frequencies for many variants across multiple individuals in per population (10 individuals in per population to calculate the allele frequencies).

[privefl]

Did you try it?