VariantTools: Tools for Working with Genetic Variants

Tools for detecting, filtering, calling, comparing and plotting variants.

AuthorMichael Lawrence, Jeremiah Degenhardt, Robert Gentleman
Date of publicationNone
MaintainerMichael Lawrence <michafla@gene.com>
LicenseArtistic-2.0
Version1.16.0

View on Bioconductor

Functions

annotateWithControlDepth Man page
calculateConcordanceMatrix Man page
calculateVariantConcordance Man page
callGenotypes Man page
CallGenotypesParam Man page
callGenotypes,TabixFile,BigWigFile-method Man page
callGenotypes,VRanges,BigWigFile-method Man page
callSampleSpecificVariants Man page
callSampleSpecificVariants,BamFile,BamFile-method Man page
callSampleSpecificVariants,character,character-method Man page
callSampleSpecificVariants,GenomicRanges,GenomicRanges-method Man page
callSampleSpecificVariants,VRanges,VRanges-method Man page
callVariantConcordance Man page
callVariants Man page
callVariants,BamFile-method Man page
callVariants,character-method Man page
callVariants,GenomicRanges-method Man page
callVariants,VRanges-method Man page
callWildtype Man page
DepthFETFilter Man page
extractCoverageForPositions Man page
matchVariants Man page
MaxControlFreqFilter Man page
minCallableCoverage Man page
MinTotalDepthFilter Man page
pileupVariants Man page
postFilterVariants Man page
qaVariants Man page
SampleSpecificVariantFilters Man page
SetdiffVariantsFilter Man page
tallyVariants Man page
tallyVariants,BamFileList-method Man page
tallyVariants,BamFile-method Man page
tallyVariants,character-method Man page
TallyVariantsParam Man page
VariantCallingFilters Man page
variantGR2Vcf Man page
\%variant_in\% Man page
\%variant_in\%,GenomicRanges,GenomicRanges-method Man page
VariantPostFilters Man page
VariantQAFilters Man page
VariantTallyParam Man page

Files

VariantTools/.BBSoptions
VariantTools/DESCRIPTION
VariantTools/NAMESPACE
VariantTools/NEWS
VariantTools/R
VariantTools/R/apply.R VariantTools/R/callGenotypes.R VariantTools/R/callVariants.R VariantTools/R/callableGenes.R VariantTools/R/cgpGr2Vcf.R VariantTools/R/diagnostics.R VariantTools/R/fisher_p.R VariantTools/R/idVerify.R VariantTools/R/pileupVariants.R VariantTools/R/postFilterVariants.R VariantTools/R/qaVariants.R VariantTools/R/sampleSpecific.R VariantTools/R/setops.R VariantTools/R/tallyVariants.R VariantTools/R/test_VariantTools_package.R VariantTools/R/transcript2genome.R VariantTools/R/utils.R VariantTools/R/variantConcordance.R VariantTools/R/wildtype.R
VariantTools/build
VariantTools/build/vignette.rds
VariantTools/inst
VariantTools/inst/doc
VariantTools/inst/doc/VariantTools.R
VariantTools/inst/doc/VariantTools.Rnw
VariantTools/inst/doc/VariantTools.pdf
VariantTools/inst/unitTests
VariantTools/inst/unitTests/test_calculateConcordanceMatrix.R
VariantTools/inst/unitTests/test_idVerify.R
VariantTools/inst/unitTests/test_variantConcordance.R
VariantTools/inst/vcf
VariantTools/inst/vcf/header.csv
VariantTools/man
VariantTools/man/FilterConstructors.Rd VariantTools/man/annnotateWithControlDepth.Rd VariantTools/man/callGenotypes.Rd VariantTools/man/callSampleSpecificVariants.Rd VariantTools/man/callVariants.Rd VariantTools/man/callWildtype.Rd VariantTools/man/concordance.Rd VariantTools/man/extractCoverageForPositions.Rd VariantTools/man/matchVariants.Rd VariantTools/man/pileupVariants.Rd VariantTools/man/postFilterVariants.Rd VariantTools/man/qaVariants.Rd VariantTools/man/tallyVariants.Rd VariantTools/man/variantGR2Vcf.Rd
VariantTools/oldman
VariantTools/oldman/TwoSampleFET.Rd
VariantTools/oldman/VEP2gr.Rd
VariantTools/oldman/annotateTrans.Rd
VariantTools/oldman/detectQuality.Rd
VariantTools/oldman/isCallable.Rd
VariantTools/oldman/plotTitv.Rd
VariantTools/oldman/variantConcordance.Rd
VariantTools/oldman/wildtype.Rd
VariantTools/scripts
VariantTools/scripts/APC_EXvR_freq.pdf
VariantTools/scripts/ATM_EXvR_freq.pdf
VariantTools/scripts/KRAS_EXvR_freq.pdf
VariantTools/scripts/KRAS_LOH.pdf
VariantTools/scripts/N_NS_RNA_EX.R
VariantTools/scripts/RAS_PATH_MUT.pdf
VariantTools/scripts/README
VariantTools/scripts/R_segfault.R
VariantTools/scripts/SNVsOmuC.Rnw
VariantTools/scripts/TN_FET.R
VariantTools/scripts/TP53_EXvR_freq.pdf
VariantTools/scripts/arraySNP_v_seq.R
VariantTools/scripts/array_het.R
VariantTools/scripts/byCoverage.R
VariantTools/scripts/check_consequences.R
VariantTools/scripts/check_damaging.R
VariantTools/scripts/check_freq_rna_ex.R
VariantTools/scripts/example_runs
VariantTools/scripts/example_runs/SAM587376_run.sh
VariantTools/scripts/example_runs/SAM587376_run_TN.sh
VariantTools/scripts/example_runs/SAM587376_varEff.sh
VariantTools/scripts/functional_vep.R
VariantTools/scripts/gastric.R
VariantTools/scripts/getAlleleByLocus_mod.R
VariantTools/scripts/getChrGRangesFromGmap.Rd
VariantTools/scripts/make_RNA_EX_gene_plot.R
VariantTools/scripts/mkRuns.R
VariantTools/scripts/mk_RASPath_gene_plot.R
VariantTools/scripts/old.variantFilter.R
VariantTools/scripts/plot_help.R
VariantTools/scripts/prob_base.R
VariantTools/scripts/rnaValRate.R
VariantTools/scripts/rnaValWrapper.R
VariantTools/scripts/run_TN_wrapper.R
VariantTools/scripts/run_callVar_wrapper.R
VariantTools/scripts/temp.R
VariantTools/scripts/testing_Rsamtools.R
VariantTools/scripts/testing_mclapply.R
VariantTools/scripts/tumor_variant_plot.R
VariantTools/scripts/variantFilter_OLD.R
VariantTools/scripts/wrap_annotate_trans.R
VariantTools/tests
VariantTools/tests/VariantTools_unit_tests.R
VariantTools/vignettes
VariantTools/vignettes/VariantTools.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.