pTuneos
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bm2-lab
pTuneos: prioritizing Tumor neoantigen from next-generation sequencing data
In the docker image, I managed to run most of the first, but there was an error in stage5. Start stage 5: neoantigen filtering using Pre&RecNeo model and refined immunogenicity...
Do you support other species, such as mice? If working with mice, which files need to be modified?
Hi~Chi Zhou! I just wonder that is it possible to provide the training data? It will help a lot! Thanks for the amazing work! Best, Liang Yi
Hi, I am running into an issue with the HLA typing that I cannot figure out. The program fails with the message: Traceback (most recent call last): File "bin/optitype_ext.py", line...
https://github.com/bm2-lab/pTuneos/blob/e6cfd0e1b57bf04fe60baee40efe4f3b0c8d56f3/src/core/VariantCallingFormat/VCFprocessor.py#L72 For INDELs, it seems that no Consequence is missense_variant ?
Some positive pMHC are missing in my pTuneos results. I think that's because of a bug in the 119 line of the neo_pyclone_annotation.py script. People should change it: from `data_drop=data_fill_na.drop_duplicates(subset=["Gene","MT_pep","WT_pep"])`...
Hi, you have a typo in your readme, the T in ptuneos should be lowercase. `Call docker pull bm2lab/pTuneos which will download the Docker image.` Cheers
