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8.8 years ago
KT
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0
Hi everyone, I am trying HLAreporter to genotype HLA from my NGS data. I cannot force HLAreporter to run properly. I have not figured out the reason yet. I am thinking of using HLAcaller but this tool is not developed and supported anymore. Does anyone know the reason why they do not support this tool? Is there anything wrong with it? Cheers KT
hi, welcome to the confusion. I have myself spent (wasted) many hours looking for an HLA prediction tool that is well maintained and transparent to use. In this regard I was super excited to see this paper and approached with high hopes to use Polysolver. Alas I had no success with its Docker-ized version. If you haven't tried it, maybe you should. As per its Nature Biotech. paper, it has impressive capabilities. I finally used HLAminer which seems ok. It has a recent version. And on a tumor sample for which we had clinical typing information available, HLAminer was correct. This was on WES
On a side note, if you want to utilize/ have RNA-seq data, then you can look to seq2hla. For the same sample we had WES on, seq2hla predicted the correct HLA type to 4 digits.
I haven't done extensive testing on many samples, but this is what I have.
Hi Amitm, Sorry for this slow response. I am sill looking for wel-maintained open HLA typing tool. I have had a look at Polysolver and HLAminer but that are all for WES data. seq2HLA works with paired-end data. My data is retieved from single-read, amplicon sequencing. So, none of these tools can be applied to my data. Thank you.