Re: [Bio-bwa-help] bwa-kit HLA

[Heng Li <lh...@me...>]

On Feb 27, 2015, at 13:35, Robert Eveleigh <rob...@mc...> wrote:

> Hi,
> 
> I am current testing the HLA protocol in bwa-kit 0.7.12.  
> 
> I have 3 questions: 
> 
> 1.  My dataset has 150bp PE reads. Are there any adjustments required in the fermi arguments?

Just use the default.

> 2.  In the *.hla.top file what is the significance of the last three numbers? i.e.
>      HLA-C*03:04:01:01       HLA-C*05:01:01:01       0       0       5

These three numbers are: #mismatches on the primary exon(s), #mismatches on all considered exons and #exons used in typing. For HLA-C, the primary exons are 2 and 3. I believe all submissions to IMGT/HLA must contain these two exons.

> 3.  Related to 2.  Are the last 3 numbers associated with the confidence of the HLA calling?  If not, is there a way to assess the confidence of the call.

For common alleles, you expect to see no mismatches. A couple of mismatches may be fine, but it will be worrying if you see more than that. It is also a good sign to see more exons used in typing. When the data quality is not good enough, you will see fewer exons typed.

Heng

> 
> Thanks your time in this.
> 
> Best,
> 
> -- 
> --------------------------------------------------------------------------------
> Robert J.M. Eveleigh, M.Sc. 
> Bioinformatics Specialist
> McGill/Genome Quebec
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