I am working on the duplicated genes in Drosophila pseudoobscura. I can found the location of duplicated genes using Flybase and Orthodb. Next, I want to make population genetics analysis of the paralogs, in which that I need to collect the variants in paralogs and checked whether it is evolve faster after duplication.
However, many of the paralogs are a young paralog which mean that there are not so many nucleotide difference between them.
Since my data is genomic reads, Is it possible to map the genetic variation precisely for each paralogs? I tried to map with bowtie2 with --verysensitive option and then following use Haplotype Caller to call the variants. However, I find many NNNN (undertermined base) following variants calling which occur in the duplicated regions. Is there any better way for mapping variants in duplicated regions in the genome?
Any help will be much appreciated