OpenVax

OpenVax v1 pipeline tutorial

OpenVax v1 is the version used to design the vaccines in the PGV-001 trials. OpenVax v2 is under active development.

The neoantigen-vaccine-pipeline runs everything from raw sequencing reads to ranked vaccine peptides inside one Docker image. You need tumor and normal whole-exome sequencing and tumor RNA-seq as gzipped FASTQ files, the patient's MHC class I alleles, and a machine with at least 16 cores. No cluster is required.

  1. Install

    docker pull openvax/neoantigen-vaccine-pipeline:latest
docker run openvax/neoantigen-vaccine-pipeline:latest -h

  2. Get a reference genome

    Processed b37decoy, GRCh38 and mm10 references are available in Google Cloud. For GRCh38:

    gsutil -m cp gs://reference-genomes/grch38.tar.gz /path/to/reference-genome/
cd /path/to/reference-genome && tar -zxvf grch38.tar.gz
chmod -R a+w grch38

  3. Set up three directories

    They are mounted as Docker volumes: /inputs holds the FASTQ files and a config file, /outputs receives results, and /reference-genome holds the reference data. All three must be world-writable, because the pipeline runs as an unprivileged user.

  4. Write a config

    A YAML file in /inputs lists the sample's files, up to six MHC class I alleles (each must be supported by NetMHCpan) and tool settings. Paths are relative to the mounted directories. Start from the example config. Paired-end reads use r1 and r2 entries with type: paired-end; data from several lanes goes in separate fragments with distinct fragment_id values.

  5. Run the test case

    The test data is a small set of reads covering the IDH1 R132H mutation, with the tumor DNA reads reused as RNA.

    cd /path/to/inputs
URL=https://github.com/openvax/neoantigen-vaccine-pipeline/raw/master
wget $URL/test/idh1_config_grch38.yaml
wget $URL/datagen/idh1_r132h_normal.fastq.gz
wget $URL/datagen/idh1_r132h_tumor.fastq.gz

docker run -it \
  -v /path/to/inputs:/inputs \
  -v /path/to/outputs:/outputs \
  -v /path/to/reference-genome:/reference-genome \
  openvax/neoantigen-vaccine-pipeline:latest \
  --configfile=/inputs/idh1_config_grch38.yaml

    The first run takes a few extra minutes while files are downloaded and cached. Results include ranked variants and vaccine peptides as text and PDF reports; the test should report a single IDH1 R132H variant.

To call somatic variants only, leave the tumor RNA and HLA alleles out of the config and the pipeline writes Mutect and Strelka VCFs instead (example config). Intermediate outputs and other options are described in the pipeline README.

Adapted from a 2020 post by Julia Kodysh.

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