Sadly, I can't not use English well....
I want to make primer for many cultivar of my subject. In my primer position, there are two bialleic SNP.
I think reason of this problem is that my subject is polyploid. I already checked that there are two bases on that posistion using bam file, IGV and bam-readcount.
What I want to know is base group(?).
If base group of reference is (A,G) and base groups that checked are (A,G) , (C,C), I can use primer that I maked using reference sequence.
I think it is similar work of haplotype phasing. Of course I'm not sure. I can't check information like this using bam-readcount. I can check it using IGV, but it takes too long. because I want check many position.
Is there any work that I check base on my target position and read name at the same time? Or is there a better way?