I have several multifasta files that contain PacBio reads of a gene of interest. I have one file of multifastas for several genotypes of a particular species. I would like to do a variant analysis on these reads but don't know where to start. Would it be possible to do the following:
- Map these reads to my original gene of interest,
- Then filter reads based on an identity score,
- Then take my filtered reads and do a variant analysis calling out SNPs or other polymorphisms between genotypes?
A GUI would be nice, but I expect to do this in R so any R-programs would be greatly appreciated. Thanks.