Statistical Genetics Software

Regression models

Understand Mixed Effect Models: Watch A Short Tutorial on Linear Mixed Model Association Testing in Genetics by Noah Zaitlen during a Winter School.

Linear mixed effect model

Generalized mixed effect model

Saige: fits generalized mixed model, imbalanced case-control outcome, rare variants
Regenie: fits generalized mixed model, fast, imbalanced case-control outcome, rare variants

PLINK

An all-in-one tool for genotype data (QC, LD, PCA, association testing, ...)
download
Input file formats: plink, bgen, gen, vcf

GCTA

Mainly heritability estimation, but also QC and PCA
download
Input file formats: binary plink files

QCTOOL

Tool to wrangle processed genetic data (bgen, gen, vcf, plink)
download: Data handling, converting file formats, combining datasets
QC
PCA
Input file formats: many (vcf, gen, bgen, plink, ...) check here

BEDTOOLS

Tool to wrangle "raw" genetic data (bed, bam, vcf, ...)
download
Cheatsheet

QUICKTEST

Association testing
download

SNPTEST

Association testing
download

emeraLD

LD estimation
download

LDstore

LD estimation
download

FINEMAP

Fine-mapping
download:
finemap howto

SumHer

SumHer
- heritability estimation
- uses summary statistics as input
- LDAK is for individual data
- see also http://dougspeed.com/heritability-model/

Misc

https://openmendel.github.io/ (statistical genetic analysis tool in Julia)
https://hail.is/ (genomic data analysis tool based on Python)
https://ritchielab.org/software/plato-download (organising, QC and analysis of genetic data)

Abbreviations

QC: Data quality control, handling, transformation
LD: Linkage disequilibrium
PCA: Principal component analysis

Webservers

GWAS Atlas: Collection of summary statistics: browse and compare GWAS results.
MR Base: A platform for Mendelian randomisation using summary data from genome-wide association studies (also has an R package).
FUMA GWAS: Functional Mapping and Annotation of Genome-Wide Association Studies. Takes summary statistics as input.
Imputation servers: Sanger Imputation Service and Michigan Imputation Server.
Locuscompare: comparison of EQTL and GWAS summary statistics (using rsid and p-values).

R packages

Packages are either hosted on CRAN or Bioconductor.

Getting started

A tutorial for implementing a GWAS in R by the Foulkes Lab.
Task view on CRAN.
R-packages that deal with genetics or genomics.

Bioconductor packages

Bioconductor
biomaRt + user guide.

CRAN packages

manhattanly for interactive Manhattan plots.
qqman: for Manhattan plots (see DYI solution in here).
rsnps: interface to SNP datasets. Check vignette.
ggman: Well done Manhattan plot in a ggplot2 look.
GWAS.utils: helper functions for genotype data and summary statistics.
gaston: genetic data handeling + modelling (variety of models)

Related to Manhattan plots:

Crafting Manhattan plots by Yan Holtz for the R graph gallery.