VariantTools: Tools for Exploratory Analysis of Variant Calls

Explore, diagnose, and compare variant calls using filters.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("VariantTools")
AuthorMichael Lawrence, Jeremiah Degenhardt, Robert Gentleman
Bioconductor views GeneticVariability Genetics Sequencing
Date of publicationNone
MaintainerMichael Lawrence <michafla@gene.com>
LicenseArtistic-2.0
Version1.18.0

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
coverage_H1993 Man page
coverage_H2073 Man page
DepthFETFilter Man page
extractCoverageForPositions Man page
genome_p53 Man page
matchVariants Man page
MaxControlFreqFilter Man page
minCallableCoverage Man page
MinTotalDepthFilter Man page
p53 Man page
pileupVariants Man page
postFilterVariants Man page
qaVariants Man page
SampleSpecificVariantFilters Man page
SetdiffVariantsFilter Man page
tallies_H1993 Man page
tallies_H2073 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

.BBSoptions
DESCRIPTION
NAMESPACE
NEWS
R
R/apply.R R/callGenotypes.R R/callVariants.R R/callableGenes.R R/cgpGr2Vcf.R R/diagnostics.R R/fisher_p.R R/idVerify.R R/pileupVariants.R R/postFilterVariants.R R/qaVariants.R R/sampleSpecific.R R/setops.R R/tallyVariants.R R/test_VariantTools_package.R R/transcript2genome.R R/utils.R R/variantConcordance.R R/wildtype.R
build
build/vignette.rds
data
data/vignette.rda
inst
inst/doc
inst/doc/VariantTools.R
inst/doc/VariantTools.Rnw
inst/doc/VariantTools.pdf
inst/doc/fig
inst/doc/fig/VariantCallingProcess.pdf
inst/doc/fig/bar-caller-freq-summary-dbSNP-count-all.pdf
inst/doc/fig/bar-fdr-cov-bin-merged-all.pdf
inst/doc/fig/bar-fnr-cov-bin-merged-all.pdf
inst/doc/fig/boxplot-altFraction.pdf
inst/doc/fig/boxplot-expected-obs-freq-source-merged-vt.pdf
inst/doc/fig/boxplot-obs-freq-sample-ceu-all.pdf
inst/doc/fig/density-altFraction.pdf
inst/doc/fig/dot-percent-recovered-caller-merged-20-all.pdf
inst/doc/fig/errors.pdf
inst/doc/fig/hist-fdr-rep-count-all.pdf
inst/doc/fig/igv_high_cov_neg.png
inst/doc/fig/mix.pdf
inst/doc/fig/post-filters.pdf
inst/doc/fig/variant-calling-filters.pdf
inst/doc/fig/workflow.pdf
inst/doc/tutorial.org
inst/doc/tutorial.pdf
inst/unitTests
inst/unitTests/test_calculateConcordanceMatrix.R inst/unitTests/test_idVerify.R inst/unitTests/test_variantConcordance.R
inst/vcf
inst/vcf/header.csv
man
man/FilterConstructors.Rd man/annnotateWithControlDepth.Rd man/callGenotypes.Rd man/callSampleSpecificVariants.Rd man/callVariants.Rd man/callWildtype.Rd man/concordance.Rd man/extractCoverageForPositions.Rd man/matchVariants.Rd man/pileupVariants.Rd man/postFilterVariants.Rd man/qaVariants.Rd man/tallyVariants.Rd man/variantGR2Vcf.Rd man/vignette.Rd
oldman
oldman/TwoSampleFET.Rd
oldman/VEP2gr.Rd
oldman/annotateTrans.Rd
oldman/detectQuality.Rd
oldman/isCallable.Rd
oldman/plotTitv.Rd
oldman/variantConcordance.Rd
oldman/wildtype.Rd
scripts
scripts/APC_EXvR_freq.pdf
scripts/ATM_EXvR_freq.pdf
scripts/KRAS_EXvR_freq.pdf
scripts/KRAS_LOH.pdf
scripts/N_NS_RNA_EX.R
scripts/RAS_PATH_MUT.pdf
scripts/README
scripts/R_segfault.R
scripts/SNVsOmuC.Rnw
scripts/TN_FET.R
scripts/TP53_EXvR_freq.pdf
scripts/arraySNP_v_seq.R scripts/array_het.R scripts/byCoverage.R scripts/check_consequences.R scripts/check_damaging.R scripts/check_freq_rna_ex.R
scripts/example_runs
scripts/example_runs/SAM587376_run.sh
scripts/example_runs/SAM587376_run_TN.sh
scripts/example_runs/SAM587376_varEff.sh
scripts/functional_vep.R scripts/gastric.R scripts/getAlleleByLocus_mod.R
scripts/getChrGRangesFromGmap.Rd
scripts/make_RNA_EX_gene_plot.R scripts/mkRuns.R scripts/mk_RASPath_gene_plot.R scripts/old.variantFilter.R scripts/plot_help.R scripts/prob_base.R scripts/rnaValRate.R scripts/rnaValWrapper.R scripts/run_TN_wrapper.R scripts/run_callVar_wrapper.R scripts/temp.R scripts/testing_Rsamtools.R scripts/testing_mclapply.R scripts/tumor_variant_plot.R scripts/variantFilter_OLD.R scripts/wrap_annotate_trans.R
tests
tests/VariantTools_unit_tests.R
vignettes
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.