Getting Started

pVACseq provides a set of example data to show the expected input and output files. You can download the data set by running the pvacseq download_example_data command.

The example data output can be reproduced by running the following command:

pvacseq run \
<example_data_dir>/annotated.expression.vcf.gz \
HCC1395_TUMOR_DNA \
HLA-A*29:02,HLA-B*45:01,DRB1*04:05 \
all \
<output_dir> \
-e1 8,9,10 \
-e2 15 \
--normal-sample-name HCC1395_NORMAL_DNA

A detailed description of all command options can be found on the Usage page.

Running pVACseq using Docker

Versioned Docker containers for pVACtools are available on DockerHub using the griffithlab/pvactools repo. The Docker container contains pVACtools as well as installations of the standalone IEDB MHC Class I and Class II software and all other supported prediction algorithms (MHCflurry, MHCnuggets, BigMHC, and DeepImmuno). Standalone IEDB is installed at /opt/iedb (--iedb-install-directory /opt/iedb).

After installing Docker you can start an interactive Docker instance by running the following command:

docker run -it griffithlab/pvactools

Version-specific images are available and can be run like so:

docker run -it griffithlab/pvactools:<version>

In order to have access to your local data inside of the Docker container you will need to mount a local volume inside of the container. This is done using the -v flag. For example, you can mount your /local/path/to/example_data_dir in your container like so:

docker run -v /local/path/to/example_data_dir:/pvactools_example_data -it griffithlab/pvactools

This will mount the example_data_dir inside the container as the /pvacseq_example_data directory. When you are inside of the container you will now have access to all of the data that was inside of the example_data_dir from the /pvaseq_example_data directory.

You will need to do the same thing for your /local/path/to/output_dir so that any output written by pVACseq will be accessible from your machine outside of your Docker container.

docker run -v /local/path/to/example_data_dir:/pvacseq_example_data -v /local/path/to/output_dir:/pvacseq_output_data -it griffithlab/pvactools

You can now run your pVACseq command like so:

pvacseq run \
/pvacseq_example_data/input.vcf \
HCC1395_TUMOR_DNA \
HLA-A*29:02,HLA-B*45:01,DRB1*04:05 \
all \
/pvacseq_output_data \
-e1 8,9,10 \
-e2 15 \
--normal-sample-name HCC1395_NORMAL_DNA
--iedb-install-directory /opt/iedb

The output from your pVACseq run can be found under /pvacseq_output_data inside of the container and /local/path/to/output_dir on your local machine.

The above example command makes use of the installations of the IEDB software in the container (--iedb-install-directory /opt/iedb).