My focus of study is on the two human homologous genes related to blood groups, which have also hybrid forms due to gene-rearrangement. I'm going to detect various polymorphisms within them. I'm thinking of aligning short reads (PE, 100bp) to these reference genes from GenBank instead of the whole reference genome (hg19). Could you please tell me what's your opinion on this issue? If you agree with me, please kindly suggest me a suitable tool?
Thanks in advance