I will be interested to calculate psi between two populations for which I have low coverage WGS data. Because of the low coverage, I don't have the right calling for each SNP, but rather the posterior probability approach implemented in ANGSD. I am wondering if there will be anyway to use a joint site frequency spectrum I have created for these two population instead of providing a bed file or SNAPP file.
Thanks !
Anne-Laure
I will be interested to calculate psi between two populations for which I have low coverage WGS data. Because of the low coverage, I don't have the right calling for each SNP, but rather the posterior probability approach implemented in ANGSD. I am wondering if there will be anyway to use a joint site frequency spectrum I have created for these two population instead of providing a bed file or SNAPP file.
Thanks !
Anne-Laure