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