pairwise population Fst calculation

[Kaustubh Adhikari]

Hi Christopher,

I have a LD-pruned genotype data file containing several populations (say from 1000 genomes), would it be possible to calculate pairwise Fst distances between each population in Plink? I initially thought the --fst flag is for this purpose, but it not, as the main .fst files gives snp-wise results and the log file only gives global fst values.

Thanks for your help.

Kaustubh.

[Christopher Chang]

This isn't directly implemented, but you should be able to compute these values with a script that cycles through all population pairs (setting them as the parameters for --keep-cluster-names).

[Kaustubh Adhikari]

Okay, understood. Thanks. Though it will be great if this can be implemented in Plink as a new functionality.