• VarScan

  • Referenced in 8 articles [sw27471]
  • based on read counts and allele frequency. Somatic variant detection. Given input from a tumor...
  • SciClone

  • Referenced in 8 articles [sw29660]
  • composition of subclones by analyzing the variant allele frequencies of somatic mutations...
  • PhyloWGS

  • Referenced in 6 articles [sw26926]
  • genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations and population...
  • rec-BTP

  • Referenced in 2 articles [sw34277]
  • subpopulations of tumor cells from the variant allele frequencies of somatic mutations...
  • SPRUCE

  • Referenced in 1 article [sw34279]
  • Specifically, the input to SPRUCE are variant allele frequencies and copy-number mixing proportions...
  • RECFMM

  • Referenced in 5 articles [sw21760]
  • supports multiple algorithm variants that mark the major advances with low-frequency interaction kernels...
  • denovolyzeR

  • Referenced in 0 articles [sw16132]
  • given population size. Observed variant frequencies can then be compared against expectation in a Poisson...
  • Kangaroo

  • Referenced in 3 articles [sw38272]
  • human colorectal cancer variant that is characterized by a high frequency of mutations in coding...
  • Canopy

  • Referenced in 0 articles [sw16685]
  • phylogenetic history. The input are variant allele frequencies (VAFs) of somatic single nucleotide alterations (SNAs...
  • SNVer

  • Referenced in 3 articles [sw36884]
  • next-generation sequencing (NGS) data. We formulate variant calling as a hypothesis testing problem ... test the significance of observed allele frequency against sequencing error. SNVer reports one single overall ... significance of a candidate locus being a variant based on which multiplicity control...
  • VarFish

  • Referenced in 1 article [sw36001]
  • multiple samples. The variants are automatically annotated with population frequencies, molecular impact, and presence ... phenotypic similarity scores. Users can filter variants based on these annotations and presumed inheritance pattern...
  • 4P

  • Referenced in 1 article [sw29496]
  • statistics (including the joint frequency spectrum) from millions of DNA variants in multiple individuals...
  • BayClone2

  • Referenced in 1 article [sw31387]
  • oldsymbol{L})), subclonal variant alleles ((oldsymbol{Z})), and the population frequencies of the subclones ((oldsymbol...
  • vipR

  • Referenced in 2 articles [sw35131]
  • variants from sequencing errors, vipR identifies sequence positions that exhibit significantly different minor allele frequencies ... technique. On a set of 82 sequence variants, vipR achieved an average sensitivity...
  • HardyWeinberg

  • Referenced in 2 articles [sw24194]
  • variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies...
  • PairClone

  • Referenced in 2 articles [sw30712]
  • only marginal reads for unpaired single‐nucleotide variants. Using Bayesian non‐parametric models, we estimate ... probabilities of the number, genotypes and population frequencies of subclones in one or more tumour...
  • Strelka

  • Referenced in 1 article [sw31866]
  • this problem so as to sensitively call variants at any practical level of tumor impurity ... novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, while...
  • GlfMultiples

  • Referenced in 1 article [sw33990]
  • generates a VCF-format set of variant calls as output. For each possible position, glfMultiples ... bases is maximized with respect to allele frequency. Decisions of which sites are polymorphic take ... assumed to account for  2/3 of all variants). glfMultiples works with log-likelihoods internally...
  • Bambino

  • Referenced in 2 articles [sw17426]
  • pooling data from multiple source files. The variant detector takes advantage of SAM-specific annotations ... database, display histograms of non-reference allele frequencies, and predict protein-coding changes caused...
  • SNVMix

  • Referenced in 4 articles [sw29569]
  • enabled whole genome and transcriptome single nucleotide variant (SNV) discovery in cancer. NGS produces millions ... capable of adjusting to deviation of allelic frequencies inherent in genomically unstable tumor genomes...