• snpQC

  • Referenced in 1 article [sw17243]
  • pipeline for quality control of Illumina SNP genotyping array data. In genome-wide association studies ... quality control (QC) of genotypes is important to avoid spurious results. It is also important ... data integrity, particularly in settings with ongoing genotyping (e.g. estimation of genomic breeding values). Here ... snpqc also builds a database to store genotypic, phenotypic and quality metrics to ensure data...
  • HTreeQA

  • Referenced in 1 article [sw20045]
  • trees in quantitative trait loci study on genotype data. With the advances in high-throughput ... genotyping technology, the study of quantitative trait loci (QTL) has emerged as a promising tool ... most existing methods are designed for homozygous genotypes, and a separate haplotype reconstruction step ... often needed to resolve heterozygous genotypes. This approach has limited power to detect nonadditive genetic...
  • TASSEL-GBS

  • Referenced in 1 article [sw23158]
  • TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. Genotyping by sequencing ... reduced representation to enable high throughput genotyping of large numbers of individuals at a large ... sequence data into SNP genotypes. The TASSEL-GBS pipeline successfully fulfills the following key design ... requiring rapid turnover from tissue collection to genotypes. Although a reference genome is required...
  • NGS

  • Referenced in 1 article [sw29692]
  • Whole genome single nucleotide polymorphism genotyping of Staphylococcus aureus. Next-generation sequencing technology enables routine ... pathogens. However, few whole genome sequencing-based genotyping pipelines are available for practical applications. Here ... genome sequencing-based single nucleotide polymorphism (SNP) genotyping method and apply to the evolutionary analysis ... methicillin-resistant Staphylococcus aureus. The SNP genotyping method calls genome variants using next-generation sequencing...
  • sparse_lowRank_regression

  • Referenced in 1 article [sw29708]
  • Longitudinal genotype-phenotype association study via temporal structure auto-learning predictive model. With rapid progress ... high-throughput genotyping and neuroimaging, imaging genetics has gained significant attention in the research ... such as Alzheimer’s Disease (AD). The genotype-phenotype association study using imaging genetic data ... presented to capture the longitudinal patterns in genotype-phenotype association study, most of them required...
  • SomaticSniper

  • Referenced in 1 article [sw31863]
  • Samtools consensus format. It uses the genotype likelihood model of MAQ (as implemented in Samtools ... probability that the tumor and normal genotypes are different. This probability is reported ... that the Tumor and Normal genotypes are not different where 0 means there ... probability that the genotypes are different and 255 means there is a probability...
  • WHICHRUN

  • Referenced in 1 article [sw08932]
  • population assignment of individuals based on multilocus genotype data. WHICHRUN, a C++ computer program that ... uses multilocus genotypic data to allocate individuals to their most likely source population, is presented ... Analysis of Mixtures (SPAM). WHICHRUN requires baseline genotype data for all potential source populations ... well as genotype data for candidate individuals for which population origin is to be determined...
  • 2SNP

  • Referenced in 1 article [sw17193]
  • scalable algorithm for haplotype inference based on genotype statistics collected only for pairs of SNPs ... arrays. As an input 2SNP takes genotype matrix and outputs the corresponding haplotype matrix ... measured by the number of correctly phased genotypes, single-site and switching errors. For example ... processor to phase 30 genotypes with 1381 SNPs (ENm010.7p15:2 data from HapMap) versus GERBIL...
  • TEA

  • Referenced in 1 article [sw09925]
  • algorithms can be combined with non-standard genotypes. Complex genotypes can be build from existing ... simple genotypes. Furthermore, non-panmictic parallel population structures like neighbourhood and multipopulation EAs are supported...
  • PedPeel

  • Referenced in 1 article [sw10511]
  • Optimal peeling order for pedigrees with incomplete genotypic information. The likelihood approach is common ... when many pedigree members have unknown genotypes. Several algorithms have been proposed to address this ... order in zero-loop pedigrees with incomplete genotypic information. It is especially useful when multiple...
  • onesamp

  • Referenced in 1 article [sw24745]
  • effective population size from one sample of genotypes has been problematic because most estimators have ... population size from a sample of microsatellite genotypes. onesamp requires an input file of sampled ... individuals’ microsatellite genotypes along with information about several sampling and biological parameters. onesamp provides...
  • SPAGEDi

  • Referenced in 2 articles [sw07534]
  • mapped individuals and/or mapped populations using genotype data of any ploidy level. It can compute...
  • FPPG

  • Referenced in 2 articles [sw10143]
  • Population Genetic Problems on Haplotypic and Genotypic Data...
  • minPtest

  • Referenced in 2 articles [sw11394]
  • huge number of single nucleotide polymorphism (SNP) genotype measurements in case-control studies. The resulting...
  • TAGster

  • Referenced in 2 articles [sw11869]
  • linkage disequilibrium (LD) tag SNPs to reduce genotyping costs. We developed a software package TAGster...
  • OMERO

  • Referenced in 2 articles [sw17002]
  • screening, electron-microscopy and even non-image-genotype data. OMERO is open-source software, available...
  • Bambino

  • Referenced in 2 articles [sw17426]
  • annotations, and produces detailed output suitable for genotyping and identification of somatic mutations. The assembly...
  • FaMoz

  • Referenced in 2 articles [sw17740]
  • real or simulated data. Error rates for genotypic mistyping can be introduced. Simulations...
  • PARENTE

  • Referenced in 2 articles [sw17741]
  • simultaneously for both potential parents, using multilocus genotypes and birth and death dates of individuals...
  • lobSTR

  • Referenced in 2 articles [sw18338]
  • reads and provides the user with the genotyping results. It is written in C/C++, includes...