• GATK

  • Referenced in 14 articles [sw12019]
  • coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework...
  • SlimGene

  • Referenced in 3 articles [sw34314]
  • along with quality-values on the base-calls). We focus on fragment-level compression, which ... minimal impact on downstream applications like SNP calling that use the quality values. Discrepancies between ... SNP calls made between the lossy and loss-less versions of the data are limited ... coverage areas where even the SNP calls made by the loss-less version are marginal...
  • BRLMM

  • Referenced in 8 articles [sw11309]
  • 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 to the RLMM (pronounced ... Currently requires seed genotypes for every SNP and sample analyzed which it obtains...
  • dChipSNP

  • Referenced in 6 articles [sw18745]
  • array replicates to make LOH calls, visualizing SNP and LOH data along chromosomes...
  • CARAT

  • Referenced in 6 articles [sw35399]
  • arrays. Results: We describe a novel algorithm called CARAT (C opy Number A nalysis with ... allele-specific output. When coupled with SNP genotype calls from the same array, CARAT provides...
  • Rsubread

  • Referenced in 2 articles [sw17316]
  • long indels, absolute expression calling and SNP calling. Can be used with reads generated from...
  • robust-scan

  • Referenced in 1 article [sw28106]
  • Tajima’s D neutrality test incorporating SNP calling and imputation uncertainties. To identify evolutionary events ... have missing data and lowconfidence SNP calls at many segregating sites. However, the traditional statistical ... confidence calls, regardless of the good SNP calls at these sites in other individuals ... which incorporates missing data and SNP-calling uncertainties. Because we do not specify any particular...
  • VarScan

  • Referenced in 6 articles [sw27471]
  • operating system. SNP, indel, and consensus calling. In addition to detecting variants, VarScan calls consensus...
  • abSNP

  • Referenced in 1 article [sw33988]
  • abSNP: RNA-Seq SNP calling in repetitive regions via abundance estimation. Variant calling, in particular ... unable to make any reliable calls. Variants in multiply mapped loci can arise, for example ... SNP caller named abSNP, which offers three innovations. (a) abSNP calls SNPs from...
  • IGV-plus

  • Referenced in 1 article [sw13252]
  • integrate a single-nucleotide polymorphism (SNP) calling software of the genome analysis toolkit (GATK...
  • IMPUTE

  • Referenced in 10 articles [sw14375]
  • program for estimating (”imputing”) unobserved genotypes in SNP association studies. The program is designed ... seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator...
  • ProbABEL

  • Referenced in 6 articles [sw10861]
  • SNP) data are frequently used in GWA analyzes. Correct analysis of imputed data calls ... analysis of genome-wide imputed SNP data and quantitative, binary, and time-till-event outcomes...
  • GenoSNP

  • Referenced in 3 articles [sw34351]
  • call genotypes by clustering allele-specific intensity data on a single nucleotide polymorphism (SNP ... genotyping algorithm for the Illumina Infinium SNP genotyping assay that is entirely within-sample ... high concordance with current methods and >99% call accuracy on HapMap samples. The ability...
  • NGS

  • Referenced in 1 article [sw29692]
  • methicillin-resistant Staphylococcus aureus. The SNP genotyping method calls genome variants using next-generation sequencing ... reveal the high-resolution whole genome SNP profiles and the structural variants of different isolates...
  • SpeedHap

  • Referenced in 2 articles [sw35353]
  • variation. The set of SNP’s present in a chromosome (called the haplotype...
  • GCTA

  • Referenced in 16 articles [sw23135]
  • report a user-friendly software tool called genome-wide complex trait analysis (GCTA), which ... than testing the association of any particular SNP to the trait. We introduce GCTA...
  • Lep-MAP

  • Referenced in 2 articles [sw20324]
  • Accurate Linkage Map Construction for Large SNP Datasets. MOTIVATION: Current high-throughput sequencing technologies allow ... called Lepidoptera-MAP (Lep-MAP), for constructing accurate linkage maps with ultradense genome-wide SNP...
  • SeqEM

  • Referenced in 1 article [sw35196]
  • simulations that SeqEM results in genotype-call error rates as small as or smaller than ... results to genotypes from an Illumina SNP array, showing that SeqEM behaves well in real ... offers an improved, robust and flexible genotype-calling approach that can be widely applied...
  • Matrix eQTL

  • Referenced in 5 articles [sw20450]
  • independent testing for association for every transcript-SNP pair. The heavy computational burden makes eQTL ... fast eQTL analysis via linear models, called Matrix eQTL. Matrix eQTL can model and test...
  • ReHap

  • Referenced in 1 article [sw35233]
  • from Shotgun Sequencing Data. Single nucleotide polymorphism (SNP) is the most common form ... SNPs present in a chromosome (called the haplotype) is of interest in a wide area...