PESCA

PESCA (proportion of population-specific and shared causal variants) is a software package for estimating proportions of population-specific and shared causal variants from GWAS summary statistics.

Software requirement

For compiling and running PESCA

To compile the PESCA program, please cd into src/, and then type make.

Data

Genome partition

We provide definitions of regions that are approximately independent in EAS and EUR here.

Reference panel

Reference panels should be in PLINK format.

We provide 1000 Genomes reference panel for EAS and EUR here. All SNPs in this reference panel have minor allele frequency greater than 5% in both populations, and have been LD pruned with \(R^2\) threshold of 0.95.

Contact

  • Huwenbo Shi: hshi_AT_hsph.harvard.edu
  • Kathy Burch: kathy.s.burch_AT_gmail.com