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I use 10 samples and analysed both by GRCH37 and GRCH38. I conpared the ***filtered.tsv and unfiltered.tsv between GRCH37 and GRCH38. The fusion genes and locations were all different. No same result…
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Dockerhub Container: mskcc/neoantigenediting:1.0
command: python /usr/bin/align_neoantigens_to_IEDB.py
The workdir needs to have the input in a `data` folder of the structure
data/id_1/id_2/Patie…
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Get a representative test set from TEMPO that we can use to test neoantigen pipeline from exome data.
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Hi,
I would like to customize the HLA input, which can be added with the optional argument -C.
I wonder about the pattern of the HLA.txt file that I should prepare for running multiple samples.
Ma…
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Is this currently supported if we input phased candidate variants?
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Hi @riederd,
Thanks for your great end-to-end tool.
I encountered an installation problem using commands below:
`mamba env create -f assets/nextNEOpi.yml`
And the error message is like:
Wou…
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Hello!
I've seen in the changelog that for DUPs the start position was changed from 0-based to 1-based. What's the case for the rest of the variants, are they 0-based or 1-based?
Best regards,
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