Files in VariantTools

Tools for Exploratory Analysis of Variant Calls

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/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/check_damaging.R scripts/APC_EXvR_freq.pdf scripts/testing_mclapply.R scripts/byCoverage.R 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/VariantTools.pdf inst/doc/tutorial.pdf inst/doc/VariantTools.R 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/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/unitTests/test_idVerify.R inst/unitTests/test_variantConcordance.R inst/unitTests/test_calculateConcordanceMatrix.R