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MathOnco / NeoPredPipe

Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
GNU Lesser General Public License v3.0
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Is there any parameter to set up multithreading? #43

Open h170607 opened 8 months ago

h170607 commented 8 months ago

hi The prediction step takes a very long time. Can the running speed be increased by increasing the number of cores?

elakatos commented 7 months ago

Hi! Unfortunately I believe that option is not available for netMHCpan 4.0 which performs the prediction. I would advise running the whole pipeline in parallel for samples, e.g. if you have multiple samples to predict for, run a separate command for each sample (a straightforward way to set this up is to have one HLA file per sample).