ImmunoTyper-SR

A Immunoglobulin Heavy Chain Variable Gene genotyping and CNV analysis tool for WGS short reads using ILP Optimization. See our BioRxiv paper here.

Installation

If you already have BWA installed and don’t want to create a new environment, just download the latest release binary (see right toolbar) and install with pip:

Then run pip install <binary.whl>

However BEST way is to setup an clean environment for the installation first (see below).

Environment and Dependencies

Installing ImmunoTyper-SR using pip will automatically install the following dependencies:

In addition to the above, you will need

BWA mem mapper. We recommend using a new conda environment for the installation, which you can also use to install BWA:

conda create -n immunotyper-SR -c bioconda python=3.8 bwa samtools
conda activate immunotyper-SR
pip install <binary.whl>

Gurobi solver configured with a valid license. Licenses are free for academic purposes.

To check that gurobi is correctly configured, run gurobi_cl from a shell.

Installing from source

If the binary fails to install for whatever reason, you can build the tool from source as follows:

conda create -n immunotyper-SR -c bioconda python=3.8 bwa samtools
conda activate immunotyper-SR
git clone git@github.com:algo-cancer/ImmunoTyper-SR.git ./ImmunoTyper-SR
cd ImmunoTyper-SR
python -m pip install --upgrade  build
python -m build
pip install dist/<.tar.gz or .whl build>

Running ImmunoTyper-SR:

After installation with pip, simply use the command immunotyper-SR. The only required input is a bam file, and output is a txt file of allele calls save in the current working direction, with the name <bam_file>-IGHV_functional_allele_calls.txt.

IMPORTANT: If your BAM was mapped to GRCh37 use the --hg37 flag.

$ immunotyper-SR --help
usage: immunotyper-SR [-h] [--output_dir OUTPUT_DIR] [--hg37] [--bwa BWA] [--max_copy MAX_COPY] [--landmarks_per_group LANDMARKS_PER_GROUP] [--landmark_groups LANDMARK_GROUPS]
                      [--stdev_coeff STDEV_COEFF] [--seq_error_rate SEQ_ERROR_RATE] [--solver_time_limit SOLVER_TIME_LIMIT] [--debug_log_path DEBUG_LOG_PATH]
                      [--write_cache_path WRITE_CACHE_PATH] [--no_coverage_estimation]
                      bam_path

ImmunoTyper-SR: Ig Genotyping using Short Read WGS

positional arguments:
  bam_path              Input BAM file

optional arguments:
  -h, --help            show this help message and exit
  --output_dir OUTPUT_DIR
                        Path to output directory. Outputs txt file of allele calls with prefix matching input BAM file name.
  --hg37                Flag if BAM mapped to GRCh37 not GRCh38
  --bwa BWA             path to bwa executible if not in $PATH
  --max_copy MAX_COPY   Maximum number of allele copies to call
  --landmarks_per_group LANDMARKS_PER_GROUP
                        Number of landmarks per group to use (default = 6)
  --landmark_groups LANDMARK_GROUPS
                        Number of landmark groups to use (default = 6)
  --stdev_coeff STDEV_COEFF
                        Standard deviation scaling coefficient (default = 1.5)
  --seq_error_rate SEQ_ERROR_RATE
                        Expected sequence error rate (default = 0.02)
  --solver_time_limit SOLVER_TIME_LIMIT
                        Time limit for ILP solver in hours
  --debug_log_path DEBUG_LOG_PATH
                        Path to write log
  --write_cache_path WRITE_CACHE_PATH
                        Specific location and name of allele db sam mapping cache
  --no_coverage_estimation
                        Disables empirical coverage