Package: varitas 0.0.2

Adam Mills

varitas: Variant Calling in Targeted Analysis Sequencing Data

Multi-caller variant analysis pipeline for targeted analysis sequencing (TAS) data. Features a modular, automated workflow that can start with raw reads and produces a user-friendly PDF summary and a spreadsheet containing consensus variant information.

Authors:Adam Mills [aut, cre], Erle Holgersen [aut], Ros Cutts [aut], Syed Haider [aut]

varitas_0.0.2.tar.gz
varitas_0.0.2.tar.gz(r-4.7-any)varitas_0.0.2.tar.gz(r-4.6-any)
varitas_0.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
varitas/json (API)

# Install 'varitas' in R:
install.packages('varitas', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.30 score 8 scripts 320 downloads 12 exports 34 dependencies

Last updated from:603e4ec1d6. Checks:2 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE149
source / vignettesOK192
linux-release-x86_64NOTE136
wasm-releaseOK171

Exports:date.stamp.file.nameget.varitas.optionsoverwrite.varitas.optionsprepare.miniseq.specificationsread.yamlrun.alignmentrun.annotationrun.post.processingrun.variant.callingrun.varitas.pipelinerun.varitas.pipeline.hybridset.varitas.options

Dependencies:assertthatclicodetoolscpp11doParalleldplyrforeachformatRfutile.loggerfutile.optionsgenericsglueiteratorslambda.rlifecyclemagrittropenxlsxpillarpkgconfigpurrrR6Rcpprlangstringistringrtibbletidyrtidyselectutf8vctrsVennDiagramwithryamlzip

What Does This Error Mean?
The Purpose of This Guide | Verifying VariTAS Options | The following stages are not supported: ____ | Solution | varitas.options must be a list of options or a string giving the path to the config YAML file | config must include reference_build | reference_build must be either grch37 or grch38 | Reference genome file ____ does not have extension .fa or .fasta | target_panel must be provided for alignment and variant calling stages | Mismatch between reference genome and target panel | Index files not found for reference genome file ____ - try running bwa index. | Sequence dictionary not found for file ____ - try running GATK CreateSequenceDictionary. | Fasta index file not found for file ____ Try running samtools faidx.
Rendered fromerrors.Rmdusingknitr::rmarkdown

Last update: 2020-11-13
Started: 2020-02-21

The VariTAS Pipeline
Pipeline Overview | Third-Party Software | Directory Structure | Stages | Alignment | Variant Calling | VarDict | MuTect | Annotation | Merging | Running the Full Pipeline | Updating Settings | Variant Filters | Solid Tumour Mode | ctDNA Mode | Examples and Use Cases | Generic Wrapper Script | Variant Calling with Matched Normal | Ion PGM Data | MiniSeq Data | Incorporating MiniSeq Variant Calls | References
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2020-11-13
Started: 2020-02-21

Readme and manuals

Help Manual

Help pageTopics
add.optionadd.option
alternate.gene.sortalternate.gene.sort
build.variant.specificationbuild.variant.specification
. Make Venn diagram of variant caller overlapcaller.overlap.venn.diagram
capitalize.callercapitalise.caller capitalize.caller
classify.variantclassify.variant
Convert output of iDES step 1 to variant call formatconvert.ides.output
create.directoriescreate.directories
date.stamp.file.namedate.stamp.file.name datestamp.file.name datestamp.filename
Extract sample IDs from file pathsextract.sample.ids
Filter variants in file.filter.variant.file
Filter variant callsfilter.variants
fix.lofreq.affix.lofreq.af
Fix variant call column namesfix.names
fix.varscan.affix.varscan.af
Get base substitutionget.base.substitution
get.bed.chromosomesget.bed.chromosomes
get.buildverget.buildver
Generate a colour schemeget.colours
Process sample coverage per amplicon dataget.coverage.by.amplicon
Get statistics about coverage per sampleget.coverage.by.sample.statistics
get.fasta.chromosomesget.fasta.chromosomes
get.file.pathget.file.path
get.filtersget.filters
get.geneget.gene
get.miniseq.sample.filesget.miniseq.sample.files
Helper function to recursively get an VariTAS optionget.option
Summarise panel coverage by geneget.panel.coverage.by.gene
Get pool corresponding to each ampliconget.pool.from.panel.data
Return VariTAS settingsget.varitas.options
get.vcf.chromosomesget.vcf.chromosomes
Check if a key is in VariTAS optionsin.varitas.options
logical.to.characterlogical.to.character
Make string with command line call from its individual componentsmake.command.line.call
mean.field.valuemean.field.value
Merge potential iDES calls with variant annotation.merge.ides.annotation
Merge variantsmerge.variants
overwrite.varitas.optionsoverwrite.varitas.options
Parse job dependenciesparse.job.dependencies
plot.amplicon.coverage.per.sampleplot.amplicon.coverage.per.sample
Plot amplicon coverage by genome orderplot.coverage.by.genome.order
plot.coverage.by.sampleplot.coverage.by.sample
plot.ontarget.percentplot.ontarget.percent
plot.paired.percentplot.paired.percent
Post-processing of variants to generate outputspost.processing
Prepare BAM specification data frame to standardized format for downstream analyses.prepare.bam.specification
prepare.fastq.specificationprepare.fastq.specification
prepare.miniseq.specificationsprepare.miniseq.specifications
prepare.vcf.specificationprepare.vcf.specification
Process coverageBed reportsprocess.coverage.reports
Process sample contamination checksprocess.sample.contamination.checks
Process total coverage statisticsprocess.total.coverage.statistics
read.all.callsread.all.calls
Read iDES outputread.ides.file
Read variant calls from file and format for ease of downstream analyses.read.variant.calls
read.yamlread.yaml
Run alignmentrun.alignment
Run alignment for a single samplerun.alignment.sample
Run all the generated bash scripts without HPC commandsrun.all.scripts
Run annotation on a set of VCF filesrun.annotation
Run ANNOVAR on a VCF filerun.annovar.vcf
Run filtering on an ANNOVAR-annotated txt filerun.filtering.txt
Run iDESrun.ides
Run LoFreq for a samplerun.lofreq.sample
Run MuSE for a samplerun.muse.sample
Run MuTect for a samplerun.mutect.sample
run.post.processingrun.post.processing
Perform sample QC by looking at target coverage.run.target.qc
Get ontarget reads and run coverage quality controlrun.target.qc.sample
run.vardict.samplerun.vardict.sample
run.variant.callingrun.variant.calling
Run VariTAS pipeline in full.run.varitas.pipeline
run.varitas.pipeline.hybridrun.varitas.pipeline.hybrid
Run VarScan for a samplerun.varscan.sample
save.configsave.config
Save coverage statistics to multi-worksheet Excel file.save.coverage.excel
Save variants to Excel.save.variants.excel
Set options for varitas pipeline.set.varitas.options
split.on.columnsplit.on.column
sum.dp4sum.dp4
Run ls commandsystem.ls
tabular.meantabular.mean
tabular.mediantabular.median
Make barplot of trinucleotide substitutionstrinucleotide.barplot
Make barplot of variants per callervariant.recurrence.barplot
Make barplot of variants per callervariants.caller.barplot
Make barplot of variants per samplevariants.sample.barplot
Check that sample specification data frame matches expected format, and that all files existverify.bam.specification
verify.bwa.indexverify.bwa.index
verify.fasta.indexverify.fasta.index
Check that FASTQ specification data frame matches expected format, and that all files existverify.fastq.specification
verify.sequence.dictionaryverify.sequence.dictionary
Check against common errors in the VariTAS options.verify.varitas.options
verify.vcf.specificationverify.vcf.specification