Dear Biostar folk!
I am now facing an issue with phasing my genotypes. I have a population data (n = 54 individuals) where a vast number of genes were sequenced for. A previous study on same species (which is a tree) shows that recombination rate should be quite high as LD exceeds rarely mare than 500 bp. SNP frequency is quite high as well like 1 in 50 bp as an average.
I was wondering if you could tell me some state-of-the-art packages/softwares dealing with the issue?
Or better to look at IER and SER measurements (after i phased the genes) and skip those genes with unresolved genotypes??
I appreciate your comments on this post and please let me know if I should write more about the data!!