can only rank the neoantigen by column **'Median Fold Change'**,

[asmlgkj]

can I select the neoantigen by the order of pvacseq output. for example , Median MT Score； Median WT Score ；Median Fold Change should I select by the Median Fold Change? and the percentile rank is all NA HH0321050101.filtered.zip

[asmlgkj]

after reading the paper of MHCnuggets. it says many times of immunogenicity in it, does pvacseq ignore the results of that. the paper name is 'High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets'

here is some sentense in it 1 We demonstrated the utility of MHCnuggets as a basic pipeline to analyze mutation immunogenicity, shared predicted IMMs, and the relationship between mutation immunogenicity, driver potential, and immune infiltrates from large-scale cancer patient sequencing data from TCGA
2 We demonstrated the utility of MHCnuggets as a basic pipeline to analyze mutation immunogenicity, shared predicted IMMs, and the relationship between mutation immunogenicity, driver potential, and immune infiltrates from large-scale cancer patient sequencing data from TCGA

[asmlgkj]

thanks a lot

would you consider add tool https://github.com/BGI2016/EPIP to gain the mutation immunogenicity