The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
How well does BWA/GATK work with sequences that are >20% divergent?
I have the genomes of several isolates of a parasite, and I would like to investigate synonymous/non-synonymous substitution for identifying potential antigens, as well as SNPs genome-wide and I am wondering how well BWA/GATK are suited for this purpose. I've been told that BWA is only very good with sequences <2% divergent, and some of the antigens in this specie are known to be >20% divergent. However, I also know that GATK does local realignments of indels. So I would specifically like to know - is BWA/GATK good for looking at substitutions/SNPs in highly variable genes, and if not which other alignment tools are compatible and appropriate for this purpose?