• ANNOVAR

  • Referenced in 3 articles [sw17295]
  • ANNOVAR: functional annotation of genetic variants from high-through put sequencing data. High-throughput sequencing ... developed the ANNOVAR tool to annotate single nucleotide variants (SNVs) and insertions/deletions, such as examining ... identifying variants reported in the 1000 Genomes Project and dbSNP. ANNOVAR can utilize annotation databases ... perform gene-based annotation and ∼15 min to perform variants reduction on 4.7 million variants...
  • SnpEff

  • Referenced in 2 articles [sw17001]
  • program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. We describe ... SnpEff, for rapidly categorizing the effects of variants in genome sequences ... Once a genome is sequenced, SnpEff annotates variants based on their genomic locations and predicts...
  • PMut

  • Referenced in 6 articles [sw31127]
  • based tool for the annotation of pathological variants on proteins, 2017 update. We present here...
  • DANN

  • Referenced in 1 article [sw31340]
  • annotating the pathogenicity of genetic variants. Annotating genetic variants, especially non-coding variants ... purpose of identifying pathogenic variants remains a challenge. Combined annotation-dependent depletion (CADD ... algorithm designed to annotate both coding and non-coding variants, and has been shown ... outperform other annotation algorithms. CADD trains a linear kernel support vector machine (SVM) to differentiate...
  • VarFish

  • Referenced in 1 article [sw36001]
  • prioritization, analysis, and user-based annotation of DNA variant data with a focus on rare ... single or multiple samples. The variants are automatically annotated with population frequencies, molecular impact ... similarity scores. Users can filter variants based on these annotations and presumed inheritance pattern ... users to create their own annotations including support for variant assessment following ACMG-AMP guidelines...
  • WEP

  • Referenced in 1 article [sw41456]
  • variant calling; 8) variant annotation; 9) result storage into custom databases to allow cross-linking ... thresholds, facilitating the identification of functionally significant variants. Default threshold values are also provided...
  • VariantAnnotation

  • Referenced in 1 article [sw17309]
  • Bioconductor package for exploration and annotation of genetic variants. Summary: VariantAnnotation is an R / Bioconductor ... package for the exploration and annotation of genetic variants. Capabilities exist for reading, writing...
  • KeBABS

  • Referenced in 1 article [sw15427]
  • included as special cases. An annotation-specific variant of the kernels uses annotation information placed...
  • Wileup

  • Referenced in 1 article [sw31858]
  • Wileup.pl: A tool for variant detection & annotation utilizing RNA-Seq data For calling ... each position is saved and evaluated to annotate them at positions were supplemental database information ... reads supporting the alternative variant are used as default thresholds. The output comprises the distribution ... position contains an SNV, and the clinical annotations from CIViC...
  • Jannovar

  • Referenced in 1 article [sw36883]
  • Jannovar: Functional variant file annotation in Java. Jannovar provides a program for the annotation...
  • svclassify

  • Referenced in 1 article [sw33141]
  • method to establish benchmark structural variant calls. Calculates annotations from one or more aligned ... class model using these annotations to classify candidate structural variants (SVs) as likely true...
  • HaploReg

  • Referenced in 2 articles [sw31869]
  • tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such ... along with chromatin state and protein binding annotation from the Roadmap Epigenomics and ENCODE projects ... hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation...
  • R453Plus1Toolbox

  • Referenced in 1 article [sw18846]
  • methods for quality assurance and annotation of detected variants. Further, a pipeline for the detection...
  • DrScheme

  • Referenced in 29 articles [sw01265]
  • tower of syntactically restricted variants of Scheme that are designed to catch typical student mistakes ... behavior of small programs. The syntax checker annotates programs with font and color changes based...
  • HAMAP

  • Referenced in 1 article [sw22977]
  • HAMAP rules allows for precise annotation of individual functional variants within large homologous protein families ... HAMAP-Scan which simplify the classification and annotation of sequences, and the incorporation...
  • Consed

  • Referenced in 2 articles [sw18793]
  • reference sequence, variant and error detection, display of annotation tracks and the ability to simultaneously...
  • GeCo++

  • Referenced in 1 article [sw33278]
  • genomic features computation and annotation in the presence of variants. Summary: We propose ... analysis algorithms easier and faster when genomic annotations and variations need to be considered...
  • Bambino

  • Referenced in 2 articles [sw17426]
  • source files. The variant detector takes advantage of SAM-specific annotations, and produces detailed output...
  • TagProp

  • Referenced in 17 articles [sw11682]
  • models for image auto-annotation. Image auto-annotation is an important open problem in computer ... words. We investigate the performance of different variants of our model and compare to existing...
  • methylKit

  • Referenced in 5 articles [sw23479]
  • package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package ... with sequencing data from RRBS and its variants, but also target-capture methods and whole...