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tatsuhikonaito / DEEP-HLA

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Preparation of input data #11

Open ni6o6 opened 1 year ago

ni6o6 commented 1 year ago

I am currently using DEEP-HLA for the first time. I have variants data analyzed by general pipeline for Whole-exome sequencing data. Could you guide me on how to create the input data? And I would also like to ask how to prepare the input data for test run.

I tried the following command as test run.

$ MODEL_DIR=./DEEP-HLA/Pan-Asian
$ python ./DEEP-HLA/impute.py --sample 1958BC --model ${MODEL_DIR}/Pan-Asian_REF.model.json --hla ${MODEL_DIR}/Pan-Asian_REF.hla.json --model-dir ${MODEL_DIR}/model --out test

I prepared a sample data "1958BC.bim" from https://software.broadinstitute.org/mpg/snp2hla/. And Then, I got a error message "No such file or directory: '1958BC.bgl.phased'". There is no such a file in the downloaded snp2hla folder and DEEP-HLA/Pan-Asia folder.

Thanks,