BWAKIT HLA Analysis

Question

[plink_9857]

Hi-

I recently used BWAKIT for HLA typing. But am having difficulty finding information that can help me interpret the output. Here are my questions and links to somewhat helpful sites.

1) What are the headers for the output file: out.hla.top?

(Snippet from my out.hla.top file):

HLA-A29:02:01:01 HLA-A31:01:02 0 0 2

HLA-B27:05:02 HLA-B44:03:01 0 0 4

2) Regarding the same output file, what does the numeric code after HLA-A* and HLA-B* represent?

HLA-A*29:02:01:01

HLA-B*27:05:02

Here are relevant links that address a similar question:

https://sourceforge.net/p/bio-bwa/mailman/message/33503064/

https://sourceforge.net/p/bio-bwa/mailman/search/?q=hla&limit=25&page=0&sort=posted_date%20desc

Answer 1

[drmaly22]

Hi,

First question

Check your first link as it contains the answer.

Second question

The numbers after HLA-A* or HLA-B* are the HLA alleles names (it is kind of coding system used in the HLA filed). To get familiar with that check out this link: http://hla.alleles.org/nomenclature/naming.html

Good luck