Package: VariantTools 1.47.0
VariantTools: Tools for Exploratory Analysis of Variant Calls
Explore, diagnose, and compare variant calls using filters.
Authors:
VariantTools_1.47.0.tar.gz
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VariantTools_1.47.0.tgz(r-4.4-any)VariantTools_1.47.0.tgz(r-4.3-any)
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VariantTools.pdf |VariantTools.html✨
VariantTools/json (API)
NEWS
# Install 'VariantTools' in R: |
install.packages('VariantTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- coverage_H1993 - Vignette Data
- coverage_H2073 - Vignette Data
- genome_p53 - Vignette Data
- p53 - Vignette Data
- tallies_H1993 - Vignette Data
- tallies_H2073 - Vignette Data
On BioConductor:VariantTools-1.47.0(bioc 3.20)VariantTools-1.46.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:6ce1d54eb5
Exports:%variant_in%annotateWithControlDepthcalculateConcordanceMatrixcalculateVariantConcordancecallGenotypesCallGenotypesParamcallSampleSpecificVariantscallVariantConcordancecallVariantscallWildtypeDepthFETFilterextractCoverageForPositionsmatchVariantsMaxControlFreqFilterminCallableCoverageMinTotalDepthFilterpileupVariantspostFilterVariantsqaVariantsSampleSpecificVariantFiltersSetdiffVariantsFiltertallyVariantsTallyVariantsParamVariantCallingFiltersvariantGR2VcfVariantPostFiltersVariantQAFilters
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsVariantAnnotationvctrsXMLXVectoryamlzlibbioc
Introduction to VariantTools
Rendered fromVariantTools.Rnw
usingutils::Sweave
on Jun 16 2024.Last update: 2017-04-24
Started: 2012-09-30
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Annotate Case with Control Depth | annotateWithControlDepth |
Call Genotypes | callGenotypes callGenotypes,TabixFile-method callGenotypes,VRanges-method CallGenotypesParam |
Call Sample-Specific Variants | callSampleSpecificVariants callSampleSpecificVariants,BamFile,BamFile-method callSampleSpecificVariants,character,character-method callSampleSpecificVariants,GenomicRanges,GenomicRanges-method callSampleSpecificVariants,VRanges,VRanges-method SampleSpecificVariantFilters |
Call Variants | callVariants callVariants,BamFile-method callVariants,character-method callVariants,GenomicRanges-method callVariants,VRanges-method VariantCallingFilters |
Calling Wildtype | callWildtype minCallableCoverage |
Variant Concordance | calculateConcordanceMatrix calculateVariantConcordance callVariantConcordance |
Get Coverage at Positions | extractCoverageForPositions |
Variant Filter Constructors | DepthFETFilter MaxControlFreqFilter MinTotalDepthFilter SetdiffVariantsFilter |
Match variants by position and allele | %variant_in% %variant_in%,GenomicRanges,GenomicRanges-method matchVariants |
Nucleotide pileup from alignments | pileupVariants |
Post-filtering of Variants | postFilterVariants VariantPostFilters |
QA Filtering of Variants | qaVariants VariantQAFilters |
Tally the positions in a BAM file | tallyVariants tallyVariants,BamFile-method tallyVariants,BamFileList-method tallyVariants,character-method TallyVariantsParam VariantTallyParam |
Create a VCF for some variants | variantGR2Vcf |
Vignette Data | coverage_H1993 coverage_H2073 genome_p53 p53 tallies_H1993 tallies_H2073 |