Geny is a tool for genotyping and calling alleles of the KIR region in the human genome from whole-genome sequencing data.
Geny needs Python 3.7+ (3.11+ recommended) and minimap2 to run.
To install Geny, just run:
pip install -r requirements.txt
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.
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
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.
Please reach out to Qinghui Zhou or Ibrahim Numanagić.