Software

  • Michigan Imputation Server (free genotype imputation service)
  • Minimac3 (computationally efficient implementation of MaCH algorithm for genotype imputation)
  • MACH (resolve long haplotypes or infer missing genotypes)

  • cleanCall (correction for DNA contamination in genotype calling)
  • LASER Software (estimate genetic ancestry on reference maps of diverse populations
  • PEDSTATS (validate and summarize pairs of pedigree and data files)
  • RELPAIR (infer relationships of pairs of individuals)
  • SIBMED (identify likely genotyping errors and mutations for a sib pair)
  • VerifyBamID (verify reads match previously known genotypes; check for contamination)

  • Asthma/eQTL (mRNA by SNP Browser provides overviews of whole-genome association studies)
  • GeneZoom (show frequency of variants in a predefined region for groups of individuals)
  • GOLD (provide graphical summary of linkage disequilibrium in human genetic data)
  • GRR (detect pedigree errors by inspecting distribution for marker allele sharing)
  • LocusZoom (plot regional association results from genome-wide association scans)
  • QPLOT (calculates summary statistics to assess the sequencing quality of sequence reads)

  • BestRepeat (variance components linkage analysis with repeated measurements)
  • FUGUE (construct haplotypes for chromosome 19 and 22 linkage disequilibrium maps)
  • Merlin (use sparse trees to represent gene flow in pedigrees)
  • QTDT (one-stop interface for family based tests of linkage disequilibrium)
  • TreeLD (infer ancestry of genomic region and analyzes for signals of disease mutations)

  • METAL (meta-analysis of large datasets in a convenient, rapid and memory efficient manner)
  • RAREMETAL (meta-analysis of rare variants from genotype arrays or sequencing

  • GREGOR (test for enrichment of list of index SNPs in experimentally annotated regulatory domains)

  • bamUtil (repository containing programs that perform operations on SAM/BAM files)
  • GotCloud (incorporate alignment and variant calling pipelines into one easy to use tool
  • FastQValidator (validate format of fastq files)

  • CNVEM (infer carrier status of CNVs in large samples of SNP genotyping data
  • CoaCC (simulate case-control study using a coalescent framework)
  • CopyMap (predict CNVs locations and allele frequencies using CGH data
  • FTEC (coalescent simulator for modeling samples from population with faster than exponential growth)
  • GENOME (rapid coalescent-based whole genome simulator)

  • CaTS (power calculations for large genetic association studies)
  • ChIP-Enrich (test ChIP-seq peak for enrichment of biological pathways)
  • EMMAX (statistical test for large scale human or model organism association mapping)
  • EPACTS (support for VCF sequence-based genotype files and PED phenotype files)
  • LAMP (extract information on genetic linkage and association)
  • p_ACT (adjust sets of p-values from association tests between correlated traits and SNPs)
  • RHMAP (radiation hybrid mapping)
  • SIMLINK (estimate power of proposed linkage study)
  • TRAFIC (association test for affected sibpairs)
  • WINNER (correct winner's curse effect in genetic association studies)