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deepomicslab / SpecHLA

SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read data.
MIT License
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Question about ploidy for LOH #9

Closed Jwong684 closed 1 year ago

Jwong684 commented 1 year ago

Hi SpecHLA developers,

Your tool has been incredibly easy to set up and use so far. I just wanted a clarification on your cal.hla.copy.pl function.

In your description you had --ploidy as "the ploidy of tumor sample in HLA gene region". What would you put if you detected focal CNV deletions or gains at different HLA regions here?

wshuai294 commented 1 year ago

Hello,

Thank you for your interest in SpecHLA. Sorry for the misleading description. The ploidy estimation is applicable to the entire tumor sample and is not specific to HLA regions. To infer the ploidy and tumor purity, we recommend utilizing software tools such as Absolute and ASCAT.

Jwong684 commented 1 year ago

Ah thank you for the clarification!