VariantTools: Tools for Working with Genetic Variants

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

Author
Michael Lawrence, Jeremiah Degenhardt, Robert Gentleman
Date of publication
None
Maintainer
Michael Lawrence <michafla@gene.com>
License
Artistic-2.0
Version
1.16.0

View on Bioconductor

Man pages

annnotateWithControlDepth
Annotate Case with Control Depth
callGenotypes
Call Genotypes
callSampleSpecificVariants
Call Sample-Specific Variants
callVariants
Call Variants
callWildtype
Calling Wildtype
concordance
Variant Concordance
extractCoverageForPositions
Get Coverage at Positions
FilterConstructors
Variant Filter Constructors
matchVariants
Match variants by position and allele
pileupVariants
Nucleotide pileup from alignments
postFilterVariants
Post-filtering of Variants
qaVariants
QA Filtering of Variants
tallyVariants
Tally the positions in a BAM file
variantGR2Vcf
Create a VCF for some variants

Files in this package

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