LDmat: efficiently queryable compression of linkage disequilibrium matrices.
LDmat: efficiently queryable compression of linkage disequilibrium matrices.
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DOI：
10.1093/bioinformatics/btad092
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发表时间：
2023-02-03
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来自大群体的连锁不平衡（LD）矩阵在群体遗传学中广泛用于精细定位、LD评分回归和全基因组关联研究（GWAS）的线性混合模型。然而，当这些矩阵来自数百万个个体时，它们可以达到很大的尺寸;因此，从大量数据中移动，共享和提取粒度信息可能很麻烦。我们试图通过开发LDmat来解决压缩和轻松查询大型LD矩阵的需求。LDmat是一个独立的工具，用于以HDF 5文件格式压缩大型LD矩阵并查询这些压缩矩阵。它可以提取对应于基因组的子区域、选择基因座的列表和次要等位基因频率范围内的基因座的子矩阵。LDmat还可以从压缩文件重建原始文件格式。LDmat是用python实现的，可以用命令'pip install ldmat'安装在Unix系统上。也可以通过https://github.com/G2Lab/ldmat和https://pypi.org/project/ldmat/访问。 补充数据可在Bioinformatics在线获得。
Linkage disequilibrium (LD) matrices derived from large populations are widely used in population genetics in fine-mapping, LD score regression, and linear mixed models for Genome-wide Association Studies (GWAS). However, these matrices can reach large sizes when they are derived from millions of individuals; hence, moving, sharing and extracting granular information from this large amount of data can be cumbersome. We sought to address the need for compressing and easily querying large LD matrices by developing LDmat. LDmat is a standalone tool to compress large LD matrices in an HDF5 file format and query these compressed matrices. It can extract submatrices corresponding to a sub-region of the genome, a list of select loci, and loci within a minor allele frequency range. LDmat can also rebuild the original file formats from the compressed files. LDmat is implemented in python, and can be installed on Unix systems with the command ‘pip install ldmat’. It can also be accessed through https://github.com/G2Lab/ldmat and https://pypi.org/project/ldmat/. Supplementary data are available at Bioinformatics online.
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影响因子：
30.8
作者：
Bulik-Sullivan, Brendan K.;Loh, Po-Ru;Finucane, Hilary K.;Ripke, Stephan;Yang, Jian;Patterson, Nick;Daly, Mark J.;Price, Alkes L.;Neale, Benjamin M.
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Neale, Benjamin M.
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