no HLA-DRB5 alleles

[DayTimeMouse]

Hi,

Thanks for developing this nice tool.

I ran the script, but the output contains no HLA-DRB5 alleles despite using both BWA and minimap2 for alignment. However, HiFi reads do cover the HLA-DRB5 region. Any ideas why this discrepancy might occur?

python SpecImmune/scripts/main.py -r hifi.fq.gz -j 40 -i HLA -n sample -o hla_minimap2 --db SpecImmune/db -y pacbio-hifi --drug_recommendation True --align_method_1 minimap2 --align_method_2 minimap2

Bset regards.

[troyeeee]

Hi,

It's usually due to low coverage or poor quality of the reads. Could you please provide the resulting output file and log file from your run? That information will help us diagnose the issue further.

Thanks.