Software/Data

gwas-pw

gwas-pw is a tool for analyzing two genome-wide association studies with the goal of identifying genetic variants associated with the two traits. The code is available here, and the model is described in Pickrell et al. (2015) Detection and interpretation of shared genetic influences on 40 human traits.
abo

Approximately independent LD blocks

The approximately independent LD blocks described in Berisa and Pickrell (2015) “Approximately independent linkage disequilibrium blocks in human populations” are available here.

GWAS Browser

The GWAS Browser, built by Tomaz, displays the publicly-available subset of the data used by Pickrell (2014) Joint analysis of functional genomic data and genome-wide association studies of 18 human traits.

fgwas

fgwas is a command line tool for integrating functional genomic data into genome-wide association studies. The code is available here, and the model is described in Pickrell (2014) Joint analysis of functional genomic data and genome-wide association studies of 18 human traits.
nrob

TreeMix

TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. We use the allele frequencies in the modern populations to infer the structure of this graph. Software is available here, and the model is described in Pickrell and Pritchard (2012) Inference of population splits and mixtures from genome-wide allele frequency data. Some extensions are presented in Pickrell et al. (2012) The genetic prehistory of southern Africa.

journal.pgen.1002967.g004

RNA-seq data and software

Some scripts for analysis of RNA-seq data, as well as the data itself, from Pickrell et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing and Pickrell et al. (2010) Noisy splicing drives mRNA isoform diversity in human cells are available from Jonathan Pritchard’s site here.

Detecting natural selection from genetic data

Scripts for calculating iHS (by Sridhar Kudaravalli), XP-EHH, and forward simulations with selection are available from the HGDP Selection Browser. This site also contains the genotype data used in Pickrell et al. (2009) Signals of recent positive selection in a worldwide sample of human populations.

Khoisan genotype data

The genotype data used by Pickrell et al. (2012) The genetic prehistory of southern Africa. and Pickrell et al. (2014) Ancient west Eurasian ancestry in southern and eastern Africa is available by request (due to the nature of the consent, the data are restricted to studies of population history). Please email the corresponding authors on the papers with a signed letter agreeing to the following restrictions:

“I affirm that
(a) I will not distribute the data outside my collaboration,
(b) I will not post it publicly,
(c) I will make no attempt to connect the genetic data to personal identifiers for the samples,
(d) I will use the data only for studies of population history,
(e) I will not use the data for any selection studies,
(f) I will not use the data for any medically or disease related analyses.
(g) I will not use the data for any commercial purposes”