1. Getting Started¶
1.1 Introduction¶
METRO takes a VCF file(s) and performs filtering and pre-processing for the pipeline input. Then, an MAF-like file containing HGVS terms describing a given mutation and a FASTA file containing transcript sequences are used to determine the consequence of a mutation on a protein product. The build sub command can be used to generate a FASTA file containing CDS sequence of each transcript. The input sub command will merge and filter MAF files based on user-provided parameters. The run sub command will parse and tokenize HGVS terms describing coding DNA mutations. METRO supports each major class of HGVS terms encoding for coding DNA mutations: substitution, deletion, insertions, duplications, and INDELS. METRO does not support HGVS tokenization of terms describing mutations in non-exonic (or non-CDS) regions like introns, 3'-UTR or 5'-UTR. METRO will mutate a given coding DNA sequence based on the provided HGVS term and will translate that sequence into an amino acid sequence. METRO will also truncate a given amino acid sequence ± N amino acids relativve to a given mutation start site. The predict sub command will take the output of the run sub command and utilize netMHCpan to make predictions related to the mutations identified. In addition, it will filter and prepare outputs based on user-provided parameters.
The following are sub-commands used within METRO:
- build: build reference files
- prepare: prepare input VAF files
- find: find mutated protein products
- predict: predict the binding of peptides to any MHC molecule
1.2 Setup Dependencies¶
METRO has two dependencies: PYTHON and netMHCpan. These dependencies can be installed by a sysadmin. Before running the pipeline or any of the commands below, please ensure PYTHON and netMHCHPan are in your $PATH.
In addition, the following PYTHON modules are required:
- argparse
- pandas
- xlrd
- numpy
CUFFLINKS
SAMTOOLS
1.3 Login to cluster¶
# ssh into cluster's head node
ssh -Y $USER@biowulf.nih.gov
1.4 Prepare an interactive node¶
# Grab an interactive node first
sinteractive
# Add PYTHON executables to $PATH
# NOTE: If you do not have a bashrc file, create one first
# Add netMHCpan executables to $PATH
# NOTE: If you do not have a bashrc file, create one first
export PATH=$PATH:/data/CCBR_Pipeliner/bin/netMHC/netMHCpan-4.1
1.5 Setup METRO through either GitHub or Docker¶
The tool is available on both GitHub or on DockerHub.
1.5.1 Clone the METRO repository from Github¶
git clone https://github.com/CCBR/METRO.git
export PATH=${PWD}/METRO:${PATH}
# run subcommands
1.5.2 Pull Docker Image¶
Review subcommands before loading singularity, as other dependencies may need to be included.¶
module load singularity
singularity shell --bind /data/$USER docker://nciccbr/ccbr_metro_v1.4 nciccbr/ccbr_metro_v1.4
# run subcommand