hla_scan report "wrong HLA gene" with bam(use hg38 as ref)

[masen1991]

When i use hla_scan on WGS data.sometimes i get wrong :ERROR: wrong HLA gene
i use :
hla_scan –b [Bam file] –v 38 –d dir_to_db/db –t 8

no matter i add -g or not ,it still wrong.
sometime it go all right.
so why do this happen?

Thank you!

[LimWChing]

Hi,
I have the same problem, it says "ERROR: wrong HLA gene". I am using fastq files as input, with the following command:
hla_scan -l [fastq1] -r [fastq2] -d path/db -t 2 -g HLA-DRB1

Does anybody has solution to this issue?

Thank you =]

[hafizmtalha]

did someone find the solution to this ??

[NourMarzouka]

I face the same issue, any clue for a solution (BAM with 38)?

[nandobonf]

the "-d" flag should point to the IMGT file. Try with "-d db/HLA-ALL.IMGT"

[miriamrainha]

hi, i have the same ERROR:wrong gene HLA.
As input fastq file because with bam file I would lost some HLA sequence.
Another important thing : What are the parameters of the bwa mem alignment? what type of reference genome does it use? This step is important because the quality of the alignment could affect the second to IMGT.