Incorrect Mutation Position value

[arosenfeld]

Installation Type

Docker

pVACtools Version / Docker Image

griffithlab/pvactools:4.0.5

Python Version

No response

Operating System

No response

Describe the bug

In some all_epitopes.tsv, the location of a mutation is incorrectly calculated for the "Mutation Position" column. For example in the attached file:

MT Epitope Seq: VAEGGRNTL
WT Epitope Seq: VAEGGPNTL
Mutation Position: 0

The mutation position should actually be 6 where P -> R.

How to reproduce this bug

The pvacseq command we ran was:

pvacseq run \
    tumor.vcf.gz \
    TUMOR \
    'HLA-A*23:01,HLA-A*32:01,HLA-B*14:01,HLA-B*44:03,HLA-C*04:01,HLA-C*08:02' \
    MHCflurry \
    out \
    --normal-sample-name NORMAL \
    --iedb-install-directory /opt/iedb \
    --run-reference-proteome-similarity \
    --peptide-fasta /Homo_sapiens.GRCh38.pep.all.fa.gz \
    -t 32 \
    -p \
    vep_phased.vcf.gz

Input files

No response

Log output

None

Output files

BUG.all_epitopes.tsv.gz

[susannasiebert]

Thank you for this bug report. #1191 reported the same issue and I'm actively working on a fix. My best guess for your case is that there is a proximal somatic variant and it's incorrectly tracking the mutation position of that variant. Would you be able to share an input VCF with just the one main somatic variant with us as well as the proximal VCF (either the full proximal VCF or one scoped to an appropriate region around the somatic variant) so that I can test my fix to ensure it also resolves your issue?