bm2lab/ptuneos repository overview

Usage:

1. Pull image from dockerhub: docker pull bm2lab/ptuneos:v2.1
2. Run the image in interactive mode with your dataset: docker run -it -v /your/path/to/dataset/:/root/data bm2lab/ptuneos:v2.1 /bin/bash
3. Change directory into /root/pTuneos: cd /root/pTuneos
4. Download reference data: bash data_hg19_download.sh for hg19 or bash data_hg38_download.sh for hg38.
5. pTuneos has two modes, WES mode and VCF mode. WES mode accepts WES and RNA-seq sequencing data as input, it conduct sequencing quality control, mutation calling, hla typing, expression profiling, neoantigen prediction, neoantigen filtering and neoantigen annotation. VCF mode accepts mutation VCF file, expression profile, copy number profile and tumor cellularity as input, it performs neoantigen prediction, neoantigen filtering and neoantigen annotation directly on input file. You should first replace the input file path in config_WES.yaml or config_VCF.yaml. Then use these two mode by: python pTuneos.py WES -i config_WES.yaml or python pTuneos.py VCF -i config_VCF.yaml

Other information about pTuneos, please refer to

1. pTunes Github repository (https://github.com/bm2-lab/pTuneos⁠)
2. Citation: Zhou, C., Wei, Z., Zhang, Z. et al. pTuneos: prioritizing tumor neoantigens from next-generation sequencing data. Genome Med 11, 67 (2019) doi:10.1186/s13073-019-0679-x