• VarScan

  • Referenced in 7 articles [sw27471]
  • addition to detecting variants, VarScan calls consensus genotypes based on read counts and allele frequency...
  • Pedcheck

  • Referenced in 4 articles [sw08985]
  • PedCheck: A Program for Identification of Genotype Incompatibilities in Linkage Analysis. Prior to performance ... data is essential. Often, identification of erroneous genotypes by visual inspection can be very difficult ... effort then required to find the erroneous genotypes and to cross-reference pedigree and marker...
  • GWAsimulator

  • Referenced in 4 articles [sw16748]
  • rapid moving-window algorithm to simulate genotype data for case-control or population samples from ... regions if desired. The program uses phased genotype data as input and has the flexibility ... simulating genotypes for different populations and different genomic SNP chips. When the HapMap phased data...
  • SimPed

  • Referenced in 3 articles [sw15080]
  • simulation program to generate haplotype and genotype data for pedigree structures. With the widespread availability ... genotype data, there is great interest in analyzing pedigree haplotype data. Intermarker linkage disequilibrium ... programs available which can generate haplotype and/or genotype data consisting of a large number ... program that quickly generates haplotype and/or genotype data for pedigrees of virtually any size...
  • ProbABEL

  • Referenced in 6 articles [sw10861]
  • implementation of specific methods which take genotype imputation uncertainty into account. Results: We developed...
  • dChipSNP

  • Referenced in 6 articles [sw18745]
  • loss-of-heterozygosity. Motivation: Oligonucleotide microarrays allow genotyping of thousands of single-nucleotide polymorphisms (SNPs...
  • UNPHASED

  • Referenced in 6 articles [sw20040]
  • quantitative traits; Maximum likelihood treatment of missing genotype data and uncertain haplotypes; Global association tests...
  • jpHMM

  • Referenced in 4 articles [sw10925]
  • assigned to one HIV-1 subtype/HBV genotype. This prediction is based on a pre-calculated ... alignment of the major HIV-1 subtypes/HBV genotypes. A detailed description of the algorithm...
  • ADMIXMAP

  • Referenced in 4 articles [sw13671]
  • Program to Model Admixture Using Marker Genotype Data. ADMIXMAP is a general-purpose program ... modelling admixture, using marker genotypes and trait data on a sample of individuals from...
  • GENEHUNTER

  • Referenced in 4 articles [sw18773]
  • computation. We use the observed pedigree genotypes to reduce the number of inheritance patterns that ... number of pedigree members available for genotyping, but typically are 10–1,000-fold, compared...
  • GEMMA

  • Referenced in 4 articles [sw23999]
  • variance in phenotypes explained (PVE) by typed genotypes (i.e. ”chip heritability”). It fits a multivariate ... Carlo (MCMC) for estimating PVE by typed genotypes, predicting phenotypes, and identifying associated markers...
  • TATES

  • Referenced in 3 articles [sw20044]
  • TATES: efficient multivariate genotype-phenotype analysis for genome-wide association studies. To date, the genome ... statistical power to detect causal variants. Multivariate genotype-phenotype methods do exist but attain maximal ... Extensive simulations, probing a wide variety of genotype-phenotype models, show that TATES’s false ... complex traits. As the actual causal genotype-phenotype model is usually unknown and probably phenotypically...
  • crlmm

  • Referenced in 3 articles [sw24830]
  • Using the R Package crlmm for Genotyping and Copy Number Estimation. Genotyping platforms such ... Affymetrix can be used to assess genotype-phenotype as well as copy number-phenotype associations ... millions of markers. While genotyping algorithms are largely concordant when assessed on HapMap samples, tools...
  • netgwas

  • Referenced in 3 articles [sw21512]
  • inter- chromosomal interactions and exploring high-dimensional genotype-phenotype (and genotypes-phenotypes-environments) network ... data (Behrouzi and Wit, 2017a), particularly in genotype-phenotype datasets. The package uses a parallelization...
  • eBURST

  • Referenced in 3 articles [sw35650]
  • Evolutionary Descent among Clusters of Related Bacterial Genotypes from Multilocus Sequence Typing Data. The introduction ... evolutionary descent among isolates with similar genotypes. Traditional clustering techniques, such as dendrograms, provide ... clonal complexes, predicts the founding (ancestral) genotype of each clonal complex, and computes the bootstrap...
  • TASSEL

  • Referenced in 5 articles [sw11446]
  • calculating diversity statistics, integration of phenotypic and genotypic data, imputing missing data and calculating principal...
  • PSMIX

  • Referenced in 5 articles [sw13670]
  • population stratification and admixture inference using multilocus genotypes and widely used in practice. However, these...
  • Matrix eQTL

  • Referenced in 5 articles [sw20450]
  • subset of transcripts and SNPs. As larger genotype and gene expression datasets become available...
  • HapBlock

  • Referenced in 5 articles [sw26434]
  • SNPs. Second, both haplotype data and genotype data from unrelated individuals and/or from general pedigrees...
  • LAMP

  • Referenced in 5 articles [sw33854]
  • described below. LAMP-LD takes the genotypes of admixed individuals as well as reference haplotype...