Package: VariantTools 1.49.0

Michael Lawrence

VariantTools: Tools for Exploratory Analysis of Variant Calls

Explore, diagnose, and compare variant calls using filters.

Authors:Michael Lawrence, Jeremiah Degenhardt, Robert Gentleman

VariantTools_1.49.0.tar.gz
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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'))

Datasets:

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-1.49.0(bioc 3.21)VariantTools-1.48.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

genetics geneticvariability sequencing

4.56 score 1 packages 40 scripts 436 downloads 15 mentions 27 exports 71 dependencies

Last updated 2 months agofrom:e6dbe11071. Checks:ERROR: 2 WARNING: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 30 2024
R-4.5-win	WARNING	Nov 30 2024
R-4.5-linux	ERROR	Nov 30 2024
R-4.4-win	WARNING	Nov 30 2024
R-4.4-mac	WARNING	Nov 30 2024
R-4.3-win	WARNING	Nov 30 2024
R-4.3-mac	WARNING	Nov 30 2024

Exports:%variant_in%annotateWithControlDepth calculateConcordanceMatrix calculateVariantConcordance callGenotypes CallGenotypesParam callSampleSpecificVariants callVariantConcordance callVariants callWildtype DepthFETFilter extractCoverageForPositions matchVariants MaxControlFreqFilter minCallableCoverage MinTotalDepthFilter pileupVariants postFilterVariants qaVariants SampleSpecificVariantFilters SetdiffVariantsFilter tallyVariants TallyVariantsParam VariantCallingFilters variantGR2Vcf VariantPostFilters VariantQAFilters

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig plogr png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils VariantAnnotation vctrs XML XVector yaml zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

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