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HLA Typing Issue about ptuneos HOT 2 OPEN

bm2-lab avatar bm2-lab commented on August 12, 2024
HLA Typing Issue

from ptuneos.

Comments (2)

ChiZhou-TJ avatar ChiZhou-TJ commented on August 12, 2024

Hi, ElizabethBorden,

Sorry for the delay. The HLA typing procedure in the pTuneos is performed by Optitype, which uses razers3 for reads mapping and extracting. As razers3 puts all mapped reads into memory, it requires large memory(>200G) if the sequencing depth of your data is deep (maybe >200X).

This issue could be handle by calling the HLA type using other tools such as POLYSOLVELR, xHLA, SOAP-HLA, hla-genotyper, HLA-HD, Kourima and, HLA-VBSeq by yourself. When you get the four-digital HLA type of your sample, you can provide it in the configure file field "hla_str". Then pTuneos would omit this procedure when running the whole pipeline.

Hope it helps!

Best,
Chi

from ptuneos.

ElizabethBorden avatar ElizabethBorden commented on August 12, 2024

That is very helpful! Thank you for your reply and I will try that!

from ptuneos.

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