MHC Class I neoantigen prediction pipeline from IM5/IM6/WES/WGS. Takes Normal .bam
and somatic .maf
and generates neoantigen predictions for HLA-A/B/C.
The pipeline has four main steps:
HGVSc
. NOTE: .maf
file should be VEP annotated using cmo_maf2maf --version 1.6.14 --vep-release 88
using this EXACT VERSION. TODO: Generate mutated sequences for fusions.is_in_wt_peptidome
column reflects that. TODO: Incorporate neoantigen quality from Lukzsa et al., Nature 2017Clone the repo and install any necessary Python libraries from requirements.txt
. This repo is currently compatible with Python 2 and 3. To install:
git clone https://github.com/taylor-lab/neoantigen-dev.git
cd neoantigen-dev
pip install -r requirements.txt
NOTE: For POLYSOLVER step, the pipeline requires 8 cores.
# Neoantigen prediction pipeline. Four main steps:
(1) Genotype HLA using POLYSOLVER,
(2) Constructed mutated peptide sequences from HGVSp/HGVSc
(3) Run NetMHC-4.0 + NetMHCpan-4.0
(4) Gather results and generate:
- <sample_id>.neoantigens.maf: original maf with neoantigen prediction columns added
- <sample_id>.all_neoantigen_predictions.txt: all the predictions made for all peptides by both the algorithms
optional arguments:
-h, --help show this help message and exit
Required arguments:
--config_file CONFIG_FILE
See: neoantigen-luna.config in the repo
--sample_id SAMPLE_ID
sample_id used to limit neoantigen prediction to
identify mutations associated with the patient in the
MAF (column 16).
--output_dir OUTPUT_DIR
output directory
--maf_file MAF_FILE expects a CMO maf file (post vcf2maf.pl)
--normal_bam NORMAL_BAM
full path to normal bam file. Either --normal_bam or
--hla_file are required.
Optional arguments:
--hla_file HLA_FILE POLYSOLVER output file (winners.hla.txt) for the
sample. If not provided,POLYSOLVER is run. Either
--normal_bam or --hla_file are required.
--peptide_lengths PEPTIDE_LENGTHS
comma-separated numbers indicating the lengths of
peptides to generate. Default: 9,10
--keep_tmp_files keeps POLYSOLVER's temporary files. for debugging
purposes. Note: TMP files can be more than 5GB.
Default: true
--force_rerun_polysolver
ignores any existing polysolver output and re-runs it.
Default: false
--force_rerun_netmhc ignores any existing netMHCpan output and re-runs it.
Default: false
<output_dir>/polysolver/winners.hla.txt
<sample_id>.neoantigens.maf. (peptide with the highest binding affinity is incorporated into the original .maf for each non-syn mutation)
<sample_id>.all_neoantigen_predictions.txt: all the predictions made for all peptides by both the algorithms
The following columns are appended to the input .maf
.
Column Name | Description |
---|---|
neo_maf_identifier_key | a unique key that can be used to find other peptides predicted for the same mutation (in .all_neoantigen_predictions.txt ) |
neo_best_icore_peptide | neopeptide sequence for the strongest binder |
neo_best_rank | binding rank for the strongest binder |
neo_best_binding_affinity | binding affinity for the strongest binder |
neo_best_binder_classification | binding classification for the strongest binder (Non Binder , Strong Binder , Weak Binder ) |
neo_best_is_in_wt_peptidome | TRUE /FALSE indicating whether the strongest binder peptide is in the reference peptidome |
neo_best_algorithm | algorithm predicting the strongest binder |
neo_best_hla_allele | hla allele for the strongest binder |
neo_n_peptides_evaluated | total # of all peptides evaluated (unique icore peptides) |
neo_n_strong_binders | total # of strong binders |
neo_n_weak_binders | total # of weak binders |
The column description for .all_neoantigen_predictions.txt
can be found in: http://www.cbs.dtu.dk/services/NetMHC/output.php. Additional columns are:
The following columns are appended to the input .maf
.
Column Name | Description |
---|---|
binder_class | Non Binder , Strong Binder (rank < 0.5 or affinity < 50 ), Weak Binder (rank < 2 or affinity < 500 ) |
best_binder_for_icore_group | TRUE /FALSE indicating if the binding prediction is the strongest among all the HLA-alleles/algorithms for the given icore peptide. |
is_in_wt_peptidome | if the peptide is present in any other protein in the entire peptidome |
neo_maf_identifier_key | a unique key that can be used to find other peptides predicted for the same mutation (in .neoantigens.maf ) |
python neoantigen.py --config_file neoantigen-luna.config \
--sample_id <sample_id> \
--normal_bam <normal.bam> \
--output_dir <output_dir> \
--maf_file <cmo_vep_annotated_maf_file>