SNP weights from covariance matrix

[Tannervanorden]

Hey!

I having been using ANGSD for a population genetics study and it has been super great. I am creating a covariance matrix using doCov 1. The output is awesome and splits all of my populations really well. My one question is if there is a way to find out which SNPs are being weighted the most by the analysis. Any help would be appreciated.

Thanks,
Tanner

[aalbrechtsen]

Using this method it is not possible since when you create the covariance matrix you loose any information of which SNPs in important.
To find out which SNPs have the highest weights my suggestion would be to either

1. use PCAngsd instead which can output the weights using the --selection options
2. extract the PC you want the weights for and then use that PC as a quantitative phenotype and perform a GWAS analysis using the -doAsso option in ANGSD