Re: [Bio-bwa-help] bwa-kit HLA
Status: Beta
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From: Heng Li <lh...@me...> - 2015-02-27 18:59:38
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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 > 740, Docteur-Penfield Ave. Rm 4200 > Montreal, Quebec, H3A 1A4, Canada > Phone: 514.398.3311 ext. 00721 > Fax: 514.398.1790 > -------------------------------------------------------------------------------- > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming The Go Parallel Website, sponsored > by Intel and developed in partnership with Slashdot Media, is your hub for all > things parallel software development, from weekly thought leadership blogs to > news, videos, case studies, tutorials and more. Take a look and join the > conversation now. http://goparallel.sourceforge.net/_______________________________________________ > Bio-bwa-help mailing list > Bio...@li... > https://lists.sourceforge.net/lists/listinfo/bio-bwa-help |