• VarScan

  • Referenced in 8 articles [sw27471]
  • read counts and allele frequency. Somatic variant detection. Given input from a tumor sample ... matched control, VarScan identifies variants and determines their somatic status (Germline, Somatic...
  • SciClone

  • Referenced in 8 articles [sw29660]
  • subclones by analyzing the variant allele frequencies of somatic mutations. We use it to detect...
  • Strelka

  • Referenced in 1 article [sw31866]
  • Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs. Motivation: Whole genome ... research. The consequent increased demand for somatic variant analysis of paired samples requires methods specialized ... this problem so as to sensitively call variants at any practical level of tumor impurity ... Results: We describe Strelka, a method for somatic SNV and small indel detection from sequencing...
  • Strelka2

  • Referenced in 1 article [sw38582]
  • accurate calling of germline and somatic variants. We describe Strelka2 (https://github.com/Illumina/strelka), an open ... source small-variant-calling method for research and clinical germline and somatic sequencing applications. Strelka2 ... somatic calling, Strelka2 substantially outperformed the current leading tools in terms of both variant-calling...
  • svmod

  • Referenced in 1 article [sw25331]
  • Finding small somatic structural variants in exome sequencing data: a machine learning approach. Genetic variation...
  • rec-BTP

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

  • Referenced in 1 article [sw34138]
  • jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants. Results: We describe ... ploidy and absolute allelic copy numbers for somatic copy number alterations (SCNAs) from tumor-normal ... modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs). Results from both in silico...
  • PhyloWGS

  • Referenced in 7 articles [sw26926]
  • subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS ... complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations...
  • SomaticSignatures

  • Referenced in 1 article [sw36881]
  • SomaticSignatures: Somatic Signatures - The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs...
  • Delly

  • Referenced in 3 articles [sw33142]
  • analysis. Motivation: The discovery of genomic structural variants (SVs) at high sensitivity and specificity ... naturally occurring variation and for understanding pathological somatic rearrangements in personal genome sequencing data...
  • Canopy

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

  • Referenced in 2 articles [sw17426]
  • pooling data from multiple source files. The variant detector takes advantage of SAM-specific annotations ... output suitable for genotyping and identification of somatic mutations. The assembly viewer can display reads...
  • SPRUCE

  • Referenced in 1 article [sw34279]
  • phylogeny describing the evolutionary history of the somatic mutations (SNVs and CNVs) of a tumor ... data. Specifically, the input to SPRUCE are variant allele frequencies and copy-number mixing proportions...
  • Socrates

  • Referenced in 1 article [sw34368]
  • soft clipped reads. Motivation: Methods for detecting somatic genome rearrangements in tumours using next-generation ... reads or split reads to predict structural variants. However, the problem remains challenging...
  • R

  • Referenced in 9832 articles [sw00771]
  • R is a language and environment for statistical...
  • GATK

  • Referenced in 17 articles [sw12019]
  • The genome analysis toolkit: a MapReduce framework for...
  • Samtools

  • Referenced in 22 articles [sw14583]
  • Samtools is a suite of programs for interacting...
  • mCSM

  • Referenced in 2 articles [sw16882]
  • mCSM: predicting the effects of mutations in proteins...
  • FastQC

  • Referenced in 8 articles [sw16946]
  • FastQC: A quality control tool for high throughput...
  • Trimmomatic

  • Referenced in 6 articles [sw17091]
  • Trimmomatic: a flexible trimmer for Illumina sequence data...