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hla_scan report "wrong HLA gene" with bam(use hg38 as ref) #3

Open masen1991 opened 3 years ago

masen1991 commented 3 years ago

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 commented 3 years ago

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 commented 1 year ago

did someone find the solution to this ??

NourMarzouka commented 1 year ago

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

nandobonf commented 1 year ago

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

miriamrainha commented 6 months ago

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.