awesome-genetics-software

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

Content

1. GWAS
2. Heritability Estimation
3. Polygenic Risk Score
4. Population Stratification

GWAS

• PLINK2 https://www.cog-genomics.org/plink/2.0/

• 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.

Heritability Estimation

• 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

• 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.

Polygenic Risk Score

• 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.

• 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.

• 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]

Population Stratification

• 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.

• 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.

• 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)

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