BindLevel results from %Rank_EL or %Rank_BA

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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BindLevel results from %Rank_EL or %Rank_BA #29

Closed wt12318 closed 3 years ago

wt12318 commented 3 years ago

Hi, The following is my output file:

According to the issue28, columns V21-V25 should be : Score_EL, %Rank_EL, Score_BA, %Rank_BA, Aff(nM).The WB BindLevel seems to be produced from %Rank_EL(>0.5 & <2); but I didn't set the --EL flag and this flag default is false. So from which column the BindLevel results are produced ? %Rank_EL or %Rank_BA?

Thank you.

elakatos commented 3 years ago

Hi, This is again I believe a difference between netMHCpan 4.0 and 4.1. I'd agree that the WB/SB tag is based on the %Rank of EL, as this is what they use by default in version 4.1. In this version the flag --BA (that we use by default in NeoPredPipe) only changes the output by adding the BA-related columns, but not what SB/WB is evaluated on (while in version 4.0 it meant WB/SB was based on BA rank). This should not be an issue for NeoPredPipe, as we directly use the WB/SB information from the software, and only require to have the Affinity value available for downstream processing in NeoRecoPo.

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