This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
Generation of haplotype or phase data for SNPs in the flanking region of STRs
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.