Getting StartedΒΆ
pVACvector provides a set of example data to show the expected input and output files. You can download the data set by running the pvacfuse download_example_data command.
There are two option as to how to run pVACvector depending on the input file type used. You can either use a pVACseq output TSV of neoepitopes or a FASTA file of peptide sequences.
Here is an example of how to run pVACvector with a pVACseq output TSV:
pvacvector run \
<example_data_dir>/input.tsv \
Test \
HLA-A*02:01,HLA-B*35:01,DRB1*11:01 \
MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign \
<output_dir> \
-e 8,9,10 \
-v <example_data_dir>/input.vcf
In this example pVACvector is run with an input FASTA file:
pvacvector run \
<example_data_dir>/input.fa \
Test \
HLA-A*02:01,HLA-B*35:01,DRB1*11:01 \
MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign \
<output_dir> \
-e 8,9,10
A detailed description of all command options can be found on the Usage page.