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SyntekabioTools / HLAscan

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Why does HLAscan report sometimes "HLAscan cannot determine proper types"? #6

Open b-niu opened 2 years ago

b-niu commented 2 years ago

Dear author, thank you for providing such an excellent HLA typing tool.

HLAscan has been working in our research all the time, but recently encountered problems in a batch of WES data. On these data, HLAscan has a high probability of reporting "HLAscan cannot determine proper types" information. The coverage depth of HLA gene was checked and there was no problem.

So may I ask that, under what circumstances will this information be reported? And is there any suggestion to adjust the parameters?

I made a docker image and run HLAscan like this:

docker run --rm -v /data:/data -w /data/NSCLC -u `id -u`:`id -g` \
hlascan:2.1.4 bash -c "hla_scan_r_v2.1.4 -d /opt/hla_scan/db/HLA-ALL.IMGT -b XXX.bam -v 37 -g HLA-A > XXX.HLA-A.txt"

An example is shown here:

===================================================== HLAscan v2.1 Report created

      1. 13:56:42

        HLA gene : HLA-A

        of considered types : 3182

    ----------- HLA-Types ----------- HLAscan cannot determine proper types

Thanks a lot.

levinyi commented 1 year ago

hi，any updates？same error.

FangmanChen commented 8 months ago

Did you solve it? I encountered the same problem.