I used Kissplice to identify SNPs in RNA-seq data without reference. I'm trying to use those SNPs for population structure analyses (admixture/structure) and for phylogenetic analyses.
I'm not sure if I have to use the output file "result_type_0.fa" or the "type_0.psl", and in either case, I don't know what is the way to change the format to ".bed" or ".vcf".
Any suggestions and comments would be very appreciated.
Thank you very much.