33ef968fef3e8a5fcc84fcc3e391bec4 *DESCRIPTION
f2a560657232b2afbdce094b763648da *NAMESPACE
302eb74005d4628313dd72f235ada0c6 *NEWS
a5b4754b8c73f7e90f735fd4f1d75429 *R/apply.R
4510516eabc3618c114c431d7bfb1f39 *R/callGenotypes.R
cff7d7af5ce48988fba8c1f98a0f9715 *R/callVariants.R
7ed032a7dfa227d168ae1ba8438bd97f *R/callableGenes.R
ea2667be56c1bef4eb2c68a86f3f4759 *R/cgpGr2Vcf.R
2232a120f2ee5da775df54c3ce612bdf *R/diagnostics.R
b83028757c00dab0ad59eabf09430a48 *R/fisher_p.R
df70bb42623c71d9910c0131f307dced *R/idVerify.R
5ba90164af61cd1c977fc9218832f5bd *R/pileupVariants.R
0b215d5e11b68918dade5210a9517d11 *R/postFilterVariants.R
0118ebfc0e2f5c59f2dcd9c930036e63 *R/qaVariants.R
901372e36b1b2f2699074772d6867ef9 *R/sampleSpecific.R
607952fde01ab44f9cfebfc3451eb5c8 *R/setops.R
6480506ab6ad720e9d9488fc7a0dd774 *R/tallyVariants.R
0d2bdd64ed2b62c5590275eae3b52f63 *R/test_VariantTools_package.R
0b52fc635ab3f81a0780b18e6a9c5924 *R/transcript2genome.R
ebf3b067ef04220613e693d7d0ed68eb *R/utils.R
49ec3c00738a7064d00b2b9093ae49f3 *R/variantConcordance.R
b66015bb0cfe5499ce6f4dae7c03d4fc *R/wildtype.R
480e5361bf5663a6ff51f9b9fcdc319d *build/vignette.rds
1694b3c9f73c5d2c12b3f98460ce4928 *data/vignette.rda
8434fa51559ad038bac4cf65303689f6 *inst/doc/VariantTools.R
b7f9d4a21e2fe40fe4373ba070ec12c4 *inst/doc/VariantTools.Rnw
f2e653a9e7b1c4bdd572e31f1e4d94d9 *inst/doc/VariantTools.pdf
e502007f6e906fa8467344cec2f4e1b6 *inst/doc/fig/VariantCallingProcess.pdf
e6a9a9d24613ddbf590543bc5ebeac0d *inst/doc/fig/bar-caller-freq-summary-dbSNP-count-all.pdf
0ea34819326314eae4c6b9d5f4ee9dbe *inst/doc/fig/bar-fdr-cov-bin-merged-all.pdf
1c91bbadcef2b6cba06c5d9b328ba192 *inst/doc/fig/bar-fnr-cov-bin-merged-all.pdf
380b2a619aefe23bd017320b0f05540f *inst/doc/fig/boxplot-altFraction.pdf
34a468a845bb92d33e20533d70da349b *inst/doc/fig/boxplot-expected-obs-freq-source-merged-vt.pdf
dc08e35af067169253e263d844fbc13f *inst/doc/fig/boxplot-obs-freq-sample-ceu-all.pdf
a6d1a91d902b823ea49e3533087adc3a *inst/doc/fig/density-altFraction.pdf
9081576fb3392c333fa126ad4557c53a *inst/doc/fig/dot-percent-recovered-caller-merged-20-all.pdf
31b854f38096fba1546ecf0124be1101 *inst/doc/fig/errors.pdf
ff7f4e378ea15116c447180c721ed35c *inst/doc/fig/hist-fdr-rep-count-all.pdf
cafe8bda6b95fb9dd48a1f3dcd14fca3 *inst/doc/fig/igv_high_cov_neg.png
72c5d2679455c4913dfc6c684c2839e2 *inst/doc/fig/mix.pdf
5192ba8e79d29bf7c9f7f2008dd7aa98 *inst/doc/fig/post-filters.pdf
c81e6de4687156b4883bdefed5c79edb *inst/doc/fig/variant-calling-filters.pdf
8360dff4ce73e85ebe879d662a8da062 *inst/doc/fig/workflow.pdf
04f3442396ed48d6be465606e784d7ca *inst/doc/tutorial.org
e18d1dc09c30c968212c5bef7d5dd6da *inst/doc/tutorial.pdf
2c4749f07b3615e481b4df89ca88d34d *inst/unitTests/test_calculateConcordanceMatrix.R
2ff6eb94487808d81e15a164c69023f1 *inst/unitTests/test_idVerify.R
cfc6d0f068fbd1c0cf8017e5aae89743 *inst/unitTests/test_variantConcordance.R
a43c2278392bc452656836bbd0ceafae *inst/vcf/header.csv
bb2feacb770c8a005679f070abaf136b *man/FilterConstructors.Rd
3c7b5d7b9ee57540494b6f2182e766b3 *man/annnotateWithControlDepth.Rd
13c3ca1bae89e14666f7a63b68c6920e *man/callGenotypes.Rd
4936ab9194e0e46d0900dd268ef3b55d *man/callSampleSpecificVariants.Rd
c3670f41c01dd5aeb43bc2a42739013c *man/callVariants.Rd
44b1136f49699fe92b58b61a0afb1ce2 *man/callWildtype.Rd
f0fe036bcdd0d30989de8f54358d823d *man/concordance.Rd
0572f9f83fc414300296b228603734b0 *man/extractCoverageForPositions.Rd
9ec2e82778f62db2151a3b7c04973712 *man/matchVariants.Rd
6665b29a53e9f8672ab513b4ecde9fba *man/pileupVariants.Rd
87befb53a0740a5c13d37b1c45c71601 *man/postFilterVariants.Rd
56b366fce20d2d6be65e1f469c9419aa *man/qaVariants.Rd
2fbaec4909f2d95a3f06f1b4b6d0d52a *man/tallyVariants.Rd
d4f544c8ecf357f2acae37c058158768 *man/variantGR2Vcf.Rd
44d991c2e15b22b7c358d6e7eb03789b *man/vignette.Rd
abfabc78b4d978bb31b5489494ebaf47 *oldman/TwoSampleFET.Rd
e5e879259f957674ce61e5dfd08d0e7a *oldman/VEP2gr.Rd
b8136524ec7a870186e7e72c2f4366f6 *oldman/annotateTrans.Rd
d4872cd785acc937eb8a6aa299fe2413 *oldman/detectQuality.Rd
dcc12b200d8013ede989f8ad7c3e4c2b *oldman/isCallable.Rd
bb9c49ac3defea0ef503cd7b7a34ad67 *oldman/plotTitv.Rd
1e174733238fe080337b45b0c5bf4b76 *oldman/variantConcordance.Rd
99889d9b089d8ad7d434ae39ea334cfd *oldman/wildtype.Rd
859ffe044798867054f86a881e6019cb *scripts/APC_EXvR_freq.pdf
09f8bcbc90782966b8a2c26707f62f83 *scripts/ATM_EXvR_freq.pdf
ece7c79c1d5fdb43acf16fd07dea79d8 *scripts/KRAS_EXvR_freq.pdf
b1078ca1f0c921d399b36ea188106570 *scripts/KRAS_LOH.pdf
08114a9692cfffa7770bfdeaa3b2ba44 *scripts/N_NS_RNA_EX.R
8041b1bb0909cdfcc83e529c28ee6d1c *scripts/RAS_PATH_MUT.pdf
4668c55ebce283e9719fe399a4a90ad0 *scripts/README
a2a8ac42716b1c9582d1845c2ec280cb *scripts/R_segfault.R
07efaad8c9f65373e2736a043b4ac019 *scripts/SNVsOmuC.Rnw
e9618b61c602c70a14074307b145c606 *scripts/TN_FET.R
186ea47c11ba23f10f697886ef2df38f *scripts/TP53_EXvR_freq.pdf
3081bfed956ce9f64fc7a92dd5e6a834 *scripts/arraySNP_v_seq.R
de4538bd4d35df3988339f7d26f8c107 *scripts/array_het.R
dbae75cc56241cd958bb6092eeae99e3 *scripts/byCoverage.R
a295038cf77b207e396b37fc9c7d7371 *scripts/check_consequences.R
d4b3891180d66e11728d2046b5bbd9a1 *scripts/check_damaging.R
f761c2dc10d9262e76b42f96a27db4df *scripts/check_freq_rna_ex.R
5e08815bb54250a113299c510096015b *scripts/example_runs/SAM587376_run.sh
bd78e615457b6369de397aeb838fa5c1 *scripts/example_runs/SAM587376_run_TN.sh
179ffc0641d7438f41cba752df419d7a *scripts/example_runs/SAM587376_varEff.sh
bcc254ecdf18a20a3f4ac5a260e408b0 *scripts/functional_vep.R
aa564b6d6ad8b61317fdec66eb041073 *scripts/gastric.R
60fb7da53171ce2be0620ee5ea23dbfd *scripts/getAlleleByLocus_mod.R
ba2591f68cdaad40b6db7de633fd59a5 *scripts/getChrGRangesFromGmap.Rd
5e4b34252a45fe9cc8217c82ebaf087b *scripts/make_RNA_EX_gene_plot.R
5032b0d2af97fe16a7aedab2e2ac8f09 *scripts/mkRuns.R
7bb8afa403ed56eb81b0f0520fab71bf *scripts/mk_RASPath_gene_plot.R
9a3d27fa80e693bf14338bf70058dde9 *scripts/old.variantFilter.R
45ca27265410808313dfb84b2d71000a *scripts/plot_help.R
0bd0643c72d8ba2695d190b5ae034bc4 *scripts/prob_base.R
8196615d24f0d9e67c0d52b1bcda37b1 *scripts/rnaValRate.R
9b63724aae167208e50de7b9455d183c *scripts/rnaValWrapper.R
2553be4193bd1c75ec910dc4343ad8e6 *scripts/run_TN_wrapper.R
3cff2535f0e69a062dad759d62a2f983 *scripts/run_callVar_wrapper.R
612bf8c580e3350201a6d2561b490d0f *scripts/temp.R
a4d6597de67e9fdc42ecaf1643f0147f *scripts/testing_Rsamtools.R
ed6b3b6ed2e78187ecfa9a9c04c3db9b *scripts/testing_mclapply.R
afb4ada0e25434f06d665ffc091878dd *scripts/tumor_variant_plot.R
ee4d8fe46867678b5b3f141d9eef59a2 *scripts/variantFilter_OLD.R
a9fd85f83dc0ba49464bc021d53e02dd *scripts/wrap_annotate_trans.R
a65a09033f23680d8554457cdaba8ab1 *tests/VariantTools_unit_tests.R
b7f9d4a21e2fe40fe4373ba070ec12c4 *vignettes/VariantTools.Rnw
