kmers_ld is a program used to compute the pairwise linkage disequilibrium (LD)
between all k-mers from a presence/absence variation (PAV) table of these
k-mers. Such a PAV table can be obtained from the filter_kmers program
of the k-mer GWAS suite of tools.
kmers_ld requires the khash.h header file from the
htslib library for functioning. Make sure
you have this library installed before compiling the program.
After downloading the software with git clone https://github.com/malemay/kmers_ld,
compiling the software is as simple as running:
cd kmers_ld
make
The kmers_ld binary can then be used with the following usage:
kmers_ld <pav_table.txt>
with the output being written to stdout.
The software can be tested by running make test. The file pav_test.txt
shows what a typicaly input PAV table should look like.
If you use this software, plase cite our publication:
Lemay, M.-A., de Ronne, M., Bélanger, R., & Belzile, F. (2023). k-mer-based GWAS enhances the discovery of causal variants and candidate genes in soybean. The Plant Genome, 16, e20374. doi:10.1002/tpg2.20374
Voichek, Y. and Weigel, D., 2020. Identifying genetic variants underlying phenotypic variation in plants without complete genomes. Nature Genetics, 52(5), pp.534-540. https://doi.org/10.1038/s41588-020-0612-7