Software

We maintain the following software packages. Please email us about any questions or suggestions you may have!

  • HESS: SNP heritability estimation at each locus in the genome while allowing for LD.
  • TWAS: Understanding the link between genetic variation to gene expression to complex traits is one of the main challenges in the field. We have developed an approach to integrate expression data with GWAS summary association statistics to identify plausible causal genes at known risk loci as well as novel risk loci.
  • PAINTOR: Finding causal variants that underlie known risk loci is one of the main post-GWAS challenges. PAINTOR is a probabilistic framework that integrates association strength with genomic functional annotation data to improve accuracy in selecting plausible causal variants for functional validation.
  • Lanc-CSV: Inferring the ancestry at each locus in the genome of recently admixed individuals (e.g. Latino Americans) plays a major role in medical and population genetic inferences ranging from finding disease risk loci to inferring recombination rates to mapping missing contigs in the human genome. Here we present a method that uses continental-specific variants (i.e. variants present in individuals from only one continental group such as Europeans or Africans) for accurate local ancestry inference. Complete description of the methods here
  • ImpG-Summary: Software package implementing methods for imputation from summary statistics and accompanying data. Version 1.0 (updated July 2013) can be downloaded here. Complete description of the methods in Pasaniuc et al “Fast and accurate imputation from summary association statistics”. Bioinformatics 2014.
  • LOCO-LD: Software package implementing methods for spatial localization of genetic samples through Linkage Disequilibrium correction. Beta Version (updated May 2013) can be downloaded here. Complete description of the methods in (10.1016/j.ajhg.2013.04.023).
  • MIXSCORE: Software package implementing methods for combining SNP association and admixture association statistics to increase power in GWAS in admixed populations. Version 1.3 (updated July 2012) can be downloaded here. Complete methods described in (10.1371/journal.pgen.1001371) with disease mapping in admixed populations reviewed in (10.1038/nrg3002).
  • LAMP: Software package for local ancestry inference in admixed populations. It takes as input genotype data from admixed samples and produces a local ancestry (chromosome painting) according to the ancestry at every locus in the genome. Several versions are included in the software package:
  • MILANC error maps: Genomic error maps in local ancestry inference inferred from Puerto Rican and Mexican trio families from the GALA data can be downloaded here. These error maps were built directly from real data without any simulation assumptions (10.1093/bioinformatics/btt166). If interested in performing local ancestry inference in your cohort using the reference panels built directly from the real GALA data please contact Bogdan (bpasaniuc_AT_mednet.ucla.edu).
  • MULTIPOP: MULTIPOP is an R program that designs follow up fine mapping studies over multiple populations. It takes as input the results of previous studies and sample haplotypes of individuals from the available follow up populations. A grid search is performed to identify the choice populations that has the highest expectation localizing the causal variant. The output is the expected rank of the causal variant for every choice of follow up populations per region and per study (10.1016/j.ajhg.2009.11.016). Download here.
  • SEQ-EM: Software for assigning short reads to homologous genes in RNA-SEQ experiments (10.1089/cmb.2010.0259). The most recent version can be downloaded here.
  • GEDI/GEDI-ADMX: The GEDI package provides methods for local ancestry inference SNP genotype error detection and correction, imputation of missing genotypes at typed SNPs, and imputation of genotypes at untyped SNPs (10.1089/cmb.2007.0133). The most recent version can be downloaded here.
  • ENT: Genotype Phasing by Entropy Minimization (10.1109/TCBB.2007.70223). The most recent version can be downloaded here.

Bibliography