• STRUCTURE

  • Referenced in 71 articles [sw13672]
  • free software package for using multi-locus genotype data to investigate population structure. Its uses...
  • PLINK

  • Referenced in 61 articles [sw04581]
  • this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through...
  • PennCNV

  • Referenced in 16 articles [sw19390]
  • number variation detection in whole-genome SNP genotyping data. Comprehensive identification and cataloging of copy ... CNVs from Illumina high-density SNP genotyping data. This algorithm incorporates multiple sources of information ... information where available. We applied PennCNV to genotyping data generated for 112 HapMap individuals ... mapping of CNVs via high-density SNP genotyping. The PennCNV software is available from...
  • Haploview

  • Referenced in 22 articles [sw11870]
  • statistics and population haplotype patterns from primary genotype data in a visually appealing and interactive...
  • R/qtl

  • Referenced in 13 articles [sw20451]
  • model (HMM) technology for dealing with missing genotype data. We have implemented the main ... algorithms, with allowance for the presence of genotyping errors, for backcrosses, intercrosses, and phase-known ... includes facilities for estimating genetic maps, identifying genotyping errors, and performing single-QTL genome scans...
  • IMPUTE

  • Referenced in 11 articles [sw14375]
  • program for estimating (”imputing”) unobserved genotypes in SNP association studies. The program is designed ... work seamlessly with the output of the genotype calling program CHIAMO and the population genetic...
  • MaCH

  • Referenced in 7 articles [sw17274]
  • MaCH: Using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genome-wide association ... SNPs must be evaluated indirectly using either genotyped markers or haplotypes thereof as proxies ... computationally efficient Markov Chain framework for genotype imputation and haplotyping in the freely available MaCH ... mosaics of each other and uses available genotype and shotgun sequence data to estimate unobserved...
  • BRLMM

  • Referenced in 8 articles [sw11309]
  • probeset-genotype is a program for making genotype calls from Affymetrix SNP microarrays. It currently ... implements three different genotype calling algorithms: BRLMM (pronounced ”B-realm”) - a model based approach similar ... extension, hence the ”B”. Currently requires seed genotypes for every SNP and sample analyzed which...
  • VanillaICE

  • Referenced in 6 articles [sw11310]
  • Hidden Markov Model for high throughput genotyping arrays. Bioconductor. Hidden Markov Models for characterizing chromosomal ... chromosomal copy numbers and the genotype (heterozygosity/homozygosity). In contrast to fluorescence in situ hybridization ... addition, measures of uncertainty for the genotype and copy number estimates can be incorporated, which...
  • oligo

  • Referenced in 9 articles [sw06102]
  • Affymetrix single-nucleotide polymorphism chips and obtaining genotype calls with the preprocessed data. We demonstrate...
  • FRANz

  • Referenced in 9 articles [sw35294]
  • robust even in the presence of genotyping errors. Availability: The C source code of FRANz...
  • GERBIL

  • Referenced in 4 articles [sw17194]
  • GERBIL: Genotype resolution and block identification using likelihood. The abundance of genotype data generated ... providing an accurate resolution (phasing) of the genotypes into haplotypes. We present here results ... method for genotype phasing in the presence of recombination. Our analysis is based ... mutations, rare recombinations, and errors. We formulate genotype resolution and block partitioning as a maximum...
  • PLASQ

  • Referenced in 6 articles [sw18746]
  • normal diploid samples, PLASQ is able to genotype with very high accuracy. Moreover ... able to provide a generalized genotype in cancer samples (e.g., CCCCT at an amplified...
  • PICNIC

  • Referenced in 6 articles [sw20386]
  • including cancer. The algorithms employed to extract genotypes and copy number variation function optimally ... model algorithm bespoke to cancer. This produces genotype classification, specification of regions of loss...
  • CARAT

  • Referenced in 6 articles [sw35399]
  • high density DNA oligonuceotide arrays designed to genotype over 100, 000 SNPs. Total and allele ... allele-specific output. When coupled with SNP genotype calls from the same array, CARAT provides...
  • MixMoGenD

  • Referenced in 5 articles [sw08624]
  • selection in model-based clustering using multilocus genotype data. We propose a variable selection procedure ... model-based clustering using multilocus genotype data. Indeed, it may happen that some loci ... associated algorithm named mixture model for genotype data (MixMoGenD) has been implemented using C++ programming...
  • admixture

  • Referenced in 5 articles [sw26449]
  • widely used to estimate population structure from genotype data in part because the computation scales ... well to whole-genome genotype data. For example, the million+ people who have taken ... modified the model to allow for genotype errors, and this seems to help convergence...
  • GenoSNP

  • Referenced in 4 articles [sw34351]
  • GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference ... population. Current genotyping algorithms typically call genotypes by clustering allele-specific intensity data ... platform. We have developed a SNP genotyping algorithm for the Illumina Infinium SNP genotyping assay ... HapMap samples. The ability to call genotypes using only within-sample information makes the method...
  • Arlequin

  • Referenced in 5 articles [sw11442]
  • estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters ... sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software...
  • CloudBurst

  • Referenced in 7 articles [sw12025]
  • variety of biological analyses including SNP discovery, genotyping and personal genomics. It is modeled after...