2fe409b3d6328361b7a9692485b934f9 *DESCRIPTION
42f28c8062ff1a7281791db2a912297a *NAMESPACE
168569c809e8d94b7a8298204adb0703 *NEWS
6c468e57b43ecb95ce45fc6e2adabad5 *R/add.option.R
fbe7f8f8b420f4d560afeed03c7d4ef0 *R/caller.overlap.venn.diagram.R
61f6e54c0488064ac12f39723b75c8b2 *R/convert.ides.output.R
fc3fda1ae8fbd21c9b4ca49ba338e595 *R/filter.variant.file.R
c9142b88f9fecee3efeac01c4860f4f8 *R/filter.variants.R
ff3b594d49655e772c2526ac99d9aafd *R/fix.names.R
539f67637dcf0beb95f3e23c7a91a335 *R/get.coverage.by.amplicon.R
65bbedcfa97c5592cb93b16c1ed1f253 *R/get.coverage.by.sample.statistics.R
5dbfffb6e5773d7d9b9b4b736446481b *R/get.filters.R
603a1589e720d0742420496d2154c818 *R/get.gene.R
1dae5b787f593ad817ecd6c99dfd9ad5 *R/get.miniseq.sample.files.R
a0d7f4e3d549322f82837a7c5841022b *R/get.option.R
71d0be48b42e7d1191c1cb32fcf81988 *R/get.varitas.options.R
db2e6b714b04849a3582e0b31eceb543 *R/helper_functions.R
d40bb42594c6f02e172238521c2d5843 *R/in.varitas.options.R
a5a811719d934703cbcb668c16fb7159 *R/merge.variants.R
d5f8a03ac5f06c16dfa005a8b3fff96a *R/overwrite.varitas.options.R
f381993ee0bf75401700e8a3239c9820 *R/plot.amplicon.coverage.per.sample.R
0358893ce95abe5925c154b94395f275 *R/plot.coverage.by.genome.order.R
8e1d10cf3af951efac8bd44255068644 *R/plot.coverage.by.sample.R
0183860395e0c0f4913afb8aa94c8da3 *R/plot.ontarget.percent.R
3f9233b8612c918b0ece68cf65d96f4e *R/plot.paired.percent.R
3ed2d89f91bdeeebea157f2b65bf94d2 *R/post.processing.R
73fef82b81545b48269b7d4798d5e195 *R/prepare.bam.specification.R
251b83b3dbe0bd4f49b8fa07ac9cfd3a *R/prepare.fastq.specification.R
e2fd10fe0a3ce0c7162dfd559d5ee8ec *R/prepare.miniseq.specifications.R
6658e901e938fc043526a1d42e1af850 *R/prepare.vcf.specification.R
6bfc8860d334371ce0e73b9a60350f4f *R/process.coverage.reports.R
741b384e981e1add45cf51eb87fe9bbe *R/process.sample.contamination.checks.R
44839c519328809b97a06b77a10c94e7 *R/process.total.coverage.statistics.R
ad6971023155933adb22206229152016 *R/read.all.calls.R
acdffe92bba2fb49842b53fbbd4d6abc *R/read.ides.file.R
53440b9337afc521f0a556a0ac705f9e *R/read.variant.calls.R
d862e757c1c36bfa7eff81f13beb2e7f *R/run.alignment.R
9b6fbbe7779de0fa7cb75c16dc18ab44 *R/run.alignment.sample.R
f67c1cf12760de187af0b007b0698ceb *R/run.all.scripts.R
7e014003e2da13cb9a83cbe28a73d9a0 *R/run.annotation.R
5874602e273659dfd08d3fe72b084547 *R/run.annovar.vcf.R
7517983e23f01c771a2220750b9688d0 *R/run.filtering.txt.R
0e5d5276b4580d8b2107cf3658d08e55 *R/run.ides.R
609f3af2246b7398c5a2ad1fb9efc567 *R/run.lofreq.sample.R
b9e09dbeac005c5602e0fdc76e064d65 *R/run.muse.sample.R
d374cb66daec529dc1248f19fb03172a *R/run.mutect.sample.R
fbdc4b0dfff46d68d91615b59a8fec84 *R/run.post.processing.R
67a001631c5fc5d8289c7e73006932e3 *R/run.target.qc.R
6aeec3865494561b9b4db33a52fbf5c7 *R/run.target.qc.sample.R
c5bf995219c303b33047ab91c0e1c0a1 *R/run.vardict.sample.R
0edbe3908b86b6a1b1cc343284a0825f *R/run.variant.calling.R
e728ef207767d86ac530c1cf131668d6 *R/run.varitas.pipeline.R
b1c4989504e903f9e88bf30368b6b331 *R/run.varitas.pipeline.hybrid.R
cc3944198f7c6eeeffd8d4c7c3f43a39 *R/run.varscan.sample.R
3f2f7544d96ca0c8922dbe8ba8a31459 *R/save.coverage.excel.R
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494fd979ef40f0c18c3bd1da0f1a68a0 *R/set.varitas.options.R
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e1f489969e9462c6ca2049a974fc8330 *R/trinucleotide.barplot.R
5aa7a5c36e5dd81f3fee8f1eee238a67 *R/variant.recurrence.barplot.R
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3770870eb2a2b501aa9204ee8fa6ab03 *R/variants.sample.barplot.R
8871b1232e0780f7edd8ed21758790dc *R/varitas-pkg.R
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2abbfa6a2aa05f8fff4b5eb6e1e5fa87 *R/verify.bwa.index.R
9e2d8f5912cb8f3ce2b9d48f1869b275 *R/verify.fasta.index.R
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2885ee9199bda25c0b665f4edbe998f0 *R/verify.varitas.options.R
da92a0d61c3954378bd9105c57657738 *R/verify.vcf.specification.R
359db88047d983b826fcf26b4e382cb0 *build/vignette.rds
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d41d8cd98f00b204e9800998ecf8427e *inst/extdata/bam/Sample_2.bam
d41d8cd98f00b204e9800998ecf8427e *inst/extdata/fastq/2018_Sample001_R1.fastq
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d41d8cd98f00b204e9800998ecf8427e *inst/extdata/fastq/2018_Sample002_R1.fastq
d41d8cd98f00b204e9800998ecf8427e *inst/extdata/fastq/2018_Sample002_R2.fastq
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d41d8cd98f00b204e9800998ecf8427e *inst/extdata/fastq/2018_Sample003_R2.fastq
d41d8cd98f00b204e9800998ecf8427e *inst/extdata/fastq/2018_Sample004_R1.fastq
d41d8cd98f00b204e9800998ecf8427e *inst/extdata/fastq/2018_Sample004_R2.fastq
74c76fbb043a3b7b4c975e6625f829e6 *inst/extdata/miniseq/Example_template.csv
d41d8cd98f00b204e9800998ecf8427e *inst/extdata/miniseq/fastq/001_S1_L001_R1_example.fastq
d41d8cd98f00b204e9800998ecf8427e *inst/extdata/miniseq/fastq/001_S1_L001_R2_example.fastq
d41d8cd98f00b204e9800998ecf8427e *inst/extdata/miniseq/fastq/002_S1_L001_R1_example.fastq
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d41d8cd98f00b204e9800998ecf8427e *inst/extdata/miniseq/isis/001_S1_example.vcf
d41d8cd98f00b204e9800998ecf8427e *inst/extdata/miniseq/isis/002_S1_example.vcf
d41d8cd98f00b204e9800998ecf8427e *inst/extdata/vcf/Sample_1.vcf
d41d8cd98f00b204e9800998ecf8427e *inst/extdata/vcf/Sample_2.vcf
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7f588923b0586340e0cf0fcf7828e4a5 *inst/report_template.Rmd
303f6190e3eb12f2d1bac7bf6bbe97b8 *inst/tumour_defaults.yaml
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0d01f42f9d4e4f47ec9d8940a0477efb *man/alternate.gene.sort.Rd
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835d22aab2daf3bf95353d65621104d6 *man/capitalize.caller.Rd
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67f5b461a382f7ac1f6bb2cc4c40ef2c *man/filter.variants.Rd
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1b8d29d9b5ba8d7f96429dd240e45905 *man/fix.varscan.af.Rd
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a8eb0716bc56f2c93fe2b546894b08f3 *man/post.processing.Rd
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5e239e7465a7309e71aa0ed1399b02a8 *vignettes/errors.Rmd
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c17960765e87301af494b32ac1383207 *vignettes/references.bib
