Output Files¶

pVACvector will create the following output files:

File Name	Description
`vector_input.fa` (optional)	An intermediate file with vaccine peptide sequences created from the epitopes in a pVACseq output file.
0…n (directory)	One numbered directory for each iteration of clipping necessary. Each one contains subdirectories for the spacers tested which in turn contain prediction information and a `junctions.tsv` intermediate result file for the attempt iteration.
`<sample_name>_results.fa`	The final output file with the peptide sequences and best spacers in the optimal order.
`junctions.tsv`	A tab-separated file listing all of the valid junctions found by pVACvector including spacer and clipping information.
`vector.png`	A PNG visualization of the above result.
`<sample_name>_results.dna.fa`	The final output file with the backtranslated DNA sequences of the included peptides and best spacers in the optimal order.
`without_<peptide_id(s)>` (directory	If no solution was found with spacers and clipping peptides, these directories contain result files for partial solutions obtained by removing peptide(s) as indicated in each directory name. These directories in turn contain a `junctions.tsv` file of all of the junctions remaining after the respective peptide(s) were removed, as well as a `<sample_name>_results.fa`, a `<sample_name>_results.dna.fa`, and a `vector.png` file if a solution was found by removing the indicated peptide(s).