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openvax / topiary

Predict mutated T-cell epitopes from sequencing data
Apache License 2.0
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mhcIIpan only outputs 1 allele #29

Closed kippakers closed 9 years ago

kippakers commented 9 years ago

It looks like topiary is losing all but one allele's epitopes when we I run with mhciipan:

topiary --mhc-predictor netmhciipan --mhc-alleles DRB1*15:01,DRB1*07:01 --maf /sc/orga/projects/PBG/TCGA/RNA/incoming/SKCM/Downloads/MAF/gdac.broadinstitute.org_SKCM.Mutation_Packager_Calls.Level_3.2014120600.0.0/TCGA-BF-A1PU-01.maf.txt --mhc-epitope-lengths 15 --self-filter-directory /sc/orga/projects/immunotherapy/peptide_prediction/human/classII/lt500/ --ic50-cutoff 500 --percentile-cutoff 100 --skip-variant-errors --output-csv data/classII/test2

outputs test2 which has 50 epitopes, all for DRB1*07:01. So I checked

topiary --mhc-predictor netmhciipan --mhc-alleles DRB1*15:01 --maf /sc/orga/projects/PBG/TCGA/RNA/incoming/SKCM/Downloads/MAF/gdac.broadinstitute.org_SKCM.Mutation_Packager_Calls.Level_3.2014120600.0.0/TCGA-BF-A1PU-01.maf.txt --mhc-epitope-lengths 15 --self-filter-directory /sc/orga/projects/immunotherapy/peptide_prediction/human/classII/lt500/ --ic50-cutoff 500 --percentile-cutoff 100 --skip-variant-errors --output-csv data/classII/test3

which gives me 36 DRB1*1501 epitopes.

iskandr commented 9 years ago

@tavinathanson Any idea what happens here?

tavinathanson commented 9 years ago

I was initially wondering if it was munging the two alleles together into one, but that wouldn't produce that output and that's not what's happening. Will look into it more after lunch!