Files in varitas
Variant Calling in Targeted Analysis Sequencing Data

MD5
NEWS
NAMESPACE
DESCRIPTION
tests/testthat.R tests/testthat/test_alignment.R tests/testthat/test_tabular.R R/helper_functions.R R/get.varitas.options.R R/prepare.fastq.specification.R R/run.all.scripts.R R/read.ides.file.R R/run.variant.calling.R R/setup.R R/get.filters.R R/run.post.processing.R R/save.coverage.excel.R R/run.lofreq.sample.R R/plot.paired.percent.R R/filter.variant.file.R R/run.alignment.sample.R R/read.variant.calls.R R/in.varitas.options.R R/run.varscan.sample.R R/plot.coverage.by.sample.R R/merge.variants.R R/verify.varitas.options.R R/process.sample.contamination.checks.R R/get.coverage.by.sample.statistics.R R/get.miniseq.sample.files.R R/verify.fastq.specification.R R/get.gene.R R/verify.sequence.dictionary.R R/plot.amplicon.coverage.per.sample.R R/process.total.coverage.statistics.R R/convert.ides.output.R R/verify.bwa.index.R R/overwrite.varitas.options.R R/caller.overlap.venn.diagram.R R/run.mutect.sample.R R/get.coverage.by.amplicon.R R/save.variants.excel.R R/prepare.miniseq.specifications.R R/run.filtering.txt.R R/prepare.bam.specification.R R/run.ides.R R/run.target.qc.sample.R R/verify.vcf.specification.R R/plot.ontarget.percent.R R/run.target.qc.R R/run.annotation.R R/add.option.R R/plot.coverage.by.genome.order.R R/set.varitas.options.R R/run.vardict.sample.R R/variants.sample.barplot.R R/process.coverage.reports.R R/trinucleotide.barplot.R R/run.muse.sample.R R/variants.caller.barplot.R R/verify.fasta.index.R R/variant.recurrence.barplot.R R/run.annovar.vcf.R R/fix.names.R R/run.varitas.pipeline.R R/prepare.vcf.specification.R R/run.varitas.pipeline.hybrid.R R/verify.bam.specification.R R/get.option.R R/varitas-pkg.R R/filter.variants.R R/read.all.calls.R R/run.alignment.R R/post.processing.R man/run.annovar.vcf.Rd man/logical.to.character.Rd man/get.filters.Rd man/read.yaml.Rd man/run.target.qc.sample.Rd man/verify.vcf.specification.Rd man/get.vcf.chromosomes.Rd man/add.option.Rd man/mean.field.value.Rd man/classify.variant.Rd man/fix.lofreq.af.Rd man/trinucleotide.barplot.Rd man/variants.caller.barplot.Rd man/get.miniseq.sample.files.Rd man/get.varitas.options.Rd man/get.colours.Rd man/plot.coverage.by.genome.order.Rd man/split.on.column.Rd man/variant.recurrence.barplot.Rd man/process.sample.contamination.checks.Rd man/get.coverage.by.sample.statistics.Rd man/prepare.fastq.specification.Rd man/run.muse.sample.Rd man/run.filtering.txt.Rd man/fix.varscan.af.Rd man/verify.fasta.index.Rd man/plot.paired.percent.Rd man/alternate.gene.sort.Rd man/run.alignment.Rd man/save.variants.excel.Rd man/tabular.mean.Rd man/variants.sample.barplot.Rd man/process.total.coverage.statistics.Rd man/verify.bam.specification.Rd man/date.stamp.file.name.Rd man/run.variant.calling.Rd man/run.varscan.sample.Rd man/fix.names.Rd man/capitalize.caller.Rd man/verify.fastq.specification.Rd man/extract.sample.ids.Rd man/get.pool.from.panel.data.Rd man/get.panel.coverage.by.gene.Rd man/run.vardict.sample.Rd man/read.ides.file.Rd man/verify.sequence.dictionary.Rd man/create.directories.Rd man/get.gene.Rd man/run.ides.Rd man/parse.job.dependencies.Rd man/prepare.miniseq.specifications.Rd man/get.file.path.Rd man/plot.ontarget.percent.Rd man/get.buildver.Rd man/make.command.line.call.Rd man/get.fasta.chromosomes.Rd man/run.target.qc.Rd man/system.ls.Rd man/get.base.substitution.Rd man/verify.varitas.options.Rd man/save.coverage.excel.Rd man/get.bed.chromosomes.Rd man/plot.amplicon.coverage.per.sample.Rd man/verify.bwa.index.Rd man/process.coverage.reports.Rd man/run.mutect.sample.Rd man/in.varitas.options.Rd man/run.all.scripts.Rd man/caller.overlap.venn.diagram.Rd man/get.option.Rd man/merge.ides.annotation.Rd man/run.lofreq.sample.Rd man/filter.variant.file.Rd man/read.all.calls.Rd man/run.varitas.pipeline.hybrid.Rd man/read.variant.calls.Rd man/plot.coverage.by.sample.Rd man/overwrite.varitas.options.Rd man/prepare.vcf.specification.Rd man/prepare.bam.specification.Rd man/merge.variants.Rd man/convert.ides.output.Rd man/tabular.median.Rd man/run.annotation.Rd man/run.varitas.pipeline.Rd man/build.variant.specification.Rd man/run.alignment.sample.Rd man/sum.dp4.Rd man/set.varitas.options.Rd man/save.config.Rd man/run.post.processing.Rd man/post.processing.Rd man/filter.variants.Rd man/get.coverage.by.amplicon.Rd
inst/ctdna_defaults.yaml
inst/config.yaml
inst/tumour_defaults.yaml
inst/report_template.Rmd
inst/ascii_logo.txt
inst/perl/run_varscan.pl
inst/perl/run_mutect.pl
inst/perl/run_iDES_sample.pl
inst/perl/run_vardict.pl
inst/perl/filter.pl
inst/perl/run_alignment.pl
inst/perl/run_annovar.pl
inst/perl/run_post_processing.pl
inst/perl/target_qc.pl
inst/perl/run_annovar_isis.pl
inst/perl/run_muse.pl
inst/perl/var2vcf_valid.pl
inst/perl/run_lofreq.pl
inst/extdata/bam/Sample_1.bam
inst/extdata/bam/Sample_2.bam
inst/extdata/vcf/Sample_2.vcf
inst/extdata/vcf/Sample_1.vcf
inst/extdata/miniseq/Example_template.csv
inst/extdata/miniseq/isis/002_S1_example.vcf
inst/extdata/miniseq/isis/001_S1_example.vcf
inst/extdata/miniseq/fastq/001_S1_L001_R1_example.fastq
inst/extdata/miniseq/fastq/001_S1_L001_R2_example.fastq
inst/extdata/miniseq/fastq/002_S1_L001_R1_example.fastq
inst/extdata/miniseq/fastq/002_S1_L001_R2_example.fastq
inst/extdata/fastq/2018_Sample003_R2.fastq
inst/extdata/fastq/2018_Sample002_R1.fastq
inst/extdata/fastq/2018_Sample004_R1.fastq
inst/extdata/fastq/2018_Sample004_R2.fastq
inst/extdata/fastq/2018_Sample003_R1.fastq
inst/extdata/fastq/2018_Sample001_R1.fastq
inst/extdata/fastq/2018_Sample001_R2.fastq
inst/extdata/fastq/2018_Sample002_R2.fastq
inst/doc/errors.R
inst/doc/introduction.html
inst/doc/errors.Rmd inst/doc/introduction.R inst/doc/introduction.Rmd
inst/doc/errors.html
build/vignette.rds
vignettes/errors.Rmd
vignettes/references.bib
vignettes/introduction.Rmd
varitas documentation built on Nov. 14, 2020, 1:07 a.m.