A list of cool software for genetic analysis and the like.
currenty in no particluar order. Please contribute.You can add to it, reorganise it..but don't delete it
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bgenie https://jmarchini.org/bgenie: A program for efficient GWAS for multiple continuous traits and PHEWAS with many features designed and optimized for large scale analysis.
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GCTA http://cnsgenomics.com/software/gcta/: GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits
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LDSC https://github.com/bulik/ldsc: ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.
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PRSice https://github.com/choishingwan/PRSice: PRSice (pronounced 'precise') is a software package for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS). PRSice can run at high-resolution to provide the best-fit PRS as well as provide results calculated at broad P-value thresholds, illustrating results corresponding to either, can thin SNPs according to linkage disequilibrium and P-value ("clumping"), and can be applied across multiple traits in a single run.
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lassosum https://github.com/tshmak/lassosum: lassosum is a method for computing LASSO estimates of a linear regression problem given summary statistics from GWAS and Genome-wide meta-analyses, accounting for Linkage Disequilibrium (LD), via a reference panel. The reference panel is assumed to be in PLINK format. Summary statistics are expected to be loaded into memory as a data.frame/data.table.
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LDpred https://github.com/bvilhjal/ldpred: LDpred is a Python based software package that adjusts GWAS summary statistics for the effects of linkage disequilibrium (LD). The details of the method is described in Vilhjalmsson et al. (AJHG 2015) [http://www.cell.com/ajhg/abstract/S0002-9297(15)00365-1]
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FlashPCA2 https://github.com/gabraham/flashpca: FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data, similar to smartpca from EIGENSOFT (http://www.hsph.harvard.edu/alkes-price/software/) and shellfish (https://github.com/dandavison/shellfish). FlashPCA is based on the https://github.com/yixuan/spectra/ library.
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ADMIXTURE https://www.genetics.ucla.edu/software/admixture/: ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.
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EIGENSOFT https://github.com/DReichLab/EIG: The EIGENSOFT package implements methods from the following 2 papers: Patterson et al. 2006 PLoS Genet 2:e190 (population structure), Price et al. 2006 Nat Genet 38:904-9 (EIGENSTRAT stratification correction)