pVACseq: Discrepancy between {sample_id}.all_epitopes.tsv and {sample_id}.fasta ?

[yiolino]

Hi, thank you for developing such an excellent software.

pVACseq: Discrepancy between {sample_id}.all_epitopes.tsv and {sample_id}.fasta ?

Description

I have successfully run pVACseq without any errors.
However, I have observed that certain peptides listed in the {sample_id}.all_epitopes.tsv are not present in the {sample_id}.fasta .

Expected Behavior

I expected that all peptides listed in the {sample_id}.all_epitopes.tsv would be included in the {sample_id}.fasta.

Actual Behavior

Certain peptides present in the {sample_id}.all_epitopes.tsv are missing from the {sample_id}.fasta.

Questions

1. Is it expected behavior that not all peptides listed in the {sample_id}.all_epitopes.tsv file are included in the {sample_id}.fasta?
2. If this is expected, could you please explain the logic behind this behavior? I am particularly interested in the section of the code in generate_protein_fasta.py here. Is my assumption correct that this part of the code is related to the observed behavior?

Additional Information

• pVACseq version: Docker 3.0.1
• OS Ubuntu 22.04

[susannasiebert]

This is generally not expected. Would you be able to share your input VCF with us for further investigation? A VCF file with just the variant in question would be sufficient for us to be able to investigate this on our end.

[yiolino]

@susannasiebert Sorry for the late reply. I have created a VCF with unnecessary information masked. I have sent it to you via email. Please check it.