ATHLATES different results with BWA-mem vs BWA-aln + sampe

[Jesse Zaretsky]

Hello,

If I run an identical script on identical input files and references, switching only my use of BWA-mem for BWA-aln-> BWA-sampe, ATHLATES will run to completion in both cases, but BWA-mem will only give one allele output, whereas I get both (and the correct ones when compared to the clinical-grade HLA testing) with aln/sampe. 

I was wondering if anyone else had encountered the same thing or might know why that is.

Thanks!
Jesse