Does anyone know of an effective way to determine haplotypes or phasing data for SNPs and STRs? I understand that STRs are inherently difficult for aligners; however, I'm trying to determine haplotypes for a large number of STRs (including the flanking region information...SNPs) on a large number of samples. So, manual verification is not really an option. We've developed an in-house perl script that calls STRs accurately; however, it currently does not include flanking region information.
Any help is greatly appreciated.