Geny 🩸☠️🦠

Geny is a tool for genotyping and calling alleles of the KIR region in the human genome from whole-genome sequencing data.

Instalation

Geny needs Python 3.7+ (3.11+ recommended) and minimap2 to run.

To install Geny, just run:

pip install -r requirements.txt

Usage

To genotype a sample, just run:

python geny.py <file.bam> -l <log.txt>

The result will be shown on the standard output and the execution log will be stored in log.txt. Example:

$ python geny.py HG01928.final.cram -l log.txt
Mapping reads: 0...5,000,000...
...
Solution:
- KIR2DL1  0030205     (support=  332)
- KIR2DL1  0030205     (support=  326)
- KIR2DL3  0010101     (support=  404)
- KIR2DL3  0010101     (support=  436)
- KIR2DL4  0010201     (support=  276)
- KIR2DL4  0010201     (support=  325)
- KIR2DP1  0020106     (support=  414)
- KIR2DP1  0020106     (support=  356)
- KIR2DS4  0010102     (support=  464)
- KIR2DS4  0010102     (support=  472)
- KIR3DL1  0150203     (support=  306)
- KIR3DL1  0250101     (support=  307)
- KIR3DL2  0020102     (support=   63)
- KIR3DL2  0020102     (support=   72)
- KIR3DL2  071         (support=   86)
- KIR3DL3  00902       (support=  187)
- KIR3DL3  00902       (support=  127)
- KIR3DP1  0030212     (support=  106)

Geny also supports CRAM files. Note that the files should be indexed and aligned to GRCh38/hg38.

If you only have FASTQ data, run Geny as:

python geny.py <file.fq> -c <coverage>

-c/--coverage is the expected coverage of the sample per chromosome. For diploid genomes, that is the total sequencing coverage divided by 2.

Parameters

usage: geny.py [-h] [-V] [-l LOG] [-c COVERAGE] [-t THREADS] file

Geny: a tool for genotyping KIR genes

positional arguments:
  file                  input BAM/CRAM/FASTA/FASTQ file

options:
  -h, --help            show this help message and exit
  -V, --version         show program's version number and exit
  -l LOG, --log LOG     log file location
  -c COVERAGE, --coverage COVERAGE
                        sample coverage
  -t THREADS, --threads THREADS
                        number of threads to use

Paper & Simulations

Geny preprint is available on bioRxiv.

Please cite:

Zhou, Q., Ghezelji, M., et al. Geny: A Genotyping Tool for Allelic Decomposition of Killer Cell Immunoglobulin-Like Receptor Genes. bioRxiv (2024). https://doi.org/10.1186/s13015-022-00210-2

Experimental data is available in paper directory.

Changelog

• Geny v1.0 (Feb 2024)

Contact

Please reach out to Qinghui Zhou or Ibrahim Numanagić.