pVACseq/bind/fuse/splice in 7.0 produce aggregated percentile metrics on three levels of granularity: binding, presentation, and immunogenicity. There are also three cutoffs --binding-percentile-threshold, --presentation-percentile-threshold, and --immunogenicity-percentile-threshold replacing the previous --percentile-threshold. A filtering/prioritizing on the combined percentile is no longer possible on those tools.
We need to decide how we want pVACvector to behave in this regard going forward. Should it continue using only the combined percentile? Or should it also have individual cutoffs? Moreover, the individual cutoffs now come with a default. Is that something we desire in pVACvector as well? Lastly, we need to discuss whether to incorporate normalized percentiles here as well.
pVACseq/bind/fuse/splice in 7.0 produce aggregated percentile metrics on three levels of granularity: binding, presentation, and immunogenicity. There are also three cutoffs
--binding-percentile-threshold,--presentation-percentile-threshold, and--immunogenicity-percentile-thresholdreplacing the previous--percentile-threshold. A filtering/prioritizing on the combined percentile is no longer possible on those tools.We need to decide how we want pVACvector to behave in this regard going forward. Should it continue using only the combined percentile? Or should it also have individual cutoffs? Moreover, the individual cutoffs now come with a default. Is that something we desire in pVACvector as well? Lastly, we need to discuss whether to incorporate normalized percentiles here as well.