Okay, I feel like this is a dumb question and that's why I haven't found a clear answer but I'll give it a go anyway.
I am interested in finding the sequences of all alelles of a specific gene of interest from NGS data of a specific genotype I'm interested in. What I have available to me is a reference genome and then illumina reads for the genotype I'm interested in. The reference genome and the illumina reads are from different genotypes but the same species. I didn't generate any of this data myself, it's just what's publically available.
I was thinking I could map the illumina reads to the reference and then blast the gene sequence from the annotated reference to the mapped reads, but I don't know how to execute this properly to get all alleles (it's a tetraploid). Would appreciate advice on the best pipeline for figuring this out.
