I am facing a problem of dealing with HLA typing using Miseq data. I want to get the HLA hyplotypes based on the Miseq data.
Using the target PCR method, we seq the target exon region which is less than the length of miseq reads, e.g., the exon=250bp, while the reads length is 300bp. In other words, the reads will cover all the exon nts.
For the diversity of the HLA hyplotypes, it is hard to directly get the results.
I have read some refs,
however, it seems that there is no direct soft to deal with such a thing. The HLACaller embeded in GATK is now unmatained by Broad institute, and the libraries have changed a lot due to the update of the HLA database.
Others suggested use the blast or mapping (bwa or bowtie) to get the results, I am trying to do such a thing, while I found that most reads can be mapped to many regions across the HLA genes, which make the results complicated to assembed into the hyplotypes.
Is there any good suggestions for this kind of data?