Man pages for varitas
Variant Calling in Targeted Analysis Sequencing Data

add.optionadd.option
alternate.gene.sortalternate.gene.sort
build.variant.specificationbuild.variant.specification
caller.overlap.venn.diagram. Make Venn diagram of variant caller overlap
capitalize.callercapitalize.caller
classify.variantclassify.variant
convert.ides.outputConvert output of iDES step 1 to variant call format
create.directoriescreate.directories
date.stamp.file.namedate.stamp.file.name
extract.sample.idsExtract sample IDs from file paths
filter.variant.fileFilter variants in file.
filter.variantsFilter variant calls
fix.lofreq.affix.lofreq.af
fix.namesFix variant call column names
fix.varscan.affix.varscan.af
get.base.substitutionGet base substitution
get.bed.chromosomesget.bed.chromosomes
get.buildverget.buildver
get.coloursGenerate a colour scheme
get.coverage.by.ampliconProcess sample coverage per amplicon data
get.coverage.by.sample.statisticsGet statistics about coverage per sample
get.fasta.chromosomesget.fasta.chromosomes
get.file.pathget.file.path
get.filtersget.filters
get.geneget.gene
get.miniseq.sample.filesget.miniseq.sample.files
get.optionHelper function to recursively get an VariTAS option
get.panel.coverage.by.geneSummarise panel coverage by gene
get.pool.from.panel.dataGet pool corresponding to each amplicon
get.varitas.optionsReturn VariTAS settings
get.vcf.chromosomesget.vcf.chromosomes
in.varitas.optionsCheck if a key is in VariTAS options
logical.to.characterlogical.to.character
make.command.line.callMake string with command line call from its individual...
mean.field.valuemean.field.value
merge.ides.annotationMerge potential iDES calls with variant annotation.
merge.variantsMerge variants
overwrite.varitas.optionsoverwrite.varitas.options
parse.job.dependenciesParse job dependencies
plot.amplicon.coverage.per.sampleplot.amplicon.coverage.per.sample
plot.coverage.by.genome.orderPlot amplicon coverage by genome order
plot.coverage.by.sampleplot.coverage.by.sample
plot.ontarget.percentplot.ontarget.percent
plot.paired.percentplot.paired.percent
post.processingPost-processing of variants to generate outputs
prepare.bam.specificationPrepare BAM specification data frame to standardized format...
prepare.fastq.specificationprepare.fastq.specification
prepare.miniseq.specificationsprepare.miniseq.specifications
prepare.vcf.specificationprepare.vcf.specification
process.coverage.reportsProcess coverageBed reports
process.sample.contamination.checksProcess sample contamination checks
process.total.coverage.statisticsProcess total coverage statistics
read.all.callsread.all.calls
read.ides.fileRead iDES output
read.variant.callsRead variant calls from file and format for ease of...
read.yamlread.yaml
run.alignmentRun alignment
run.alignment.sampleRun alignment for a single sample
run.all.scriptsRun all the generated bash scripts without HPC commands
run.annotationRun annotation on a set of VCF files
run.annovar.vcfRun ANNOVAR on a VCF file
run.filtering.txtRun filtering on an ANNOVAR-annotated txt file
run.idesRun iDES
run.lofreq.sampleRun LoFreq for a sample
run.muse.sampleRun MuSE for a sample
run.mutect.sampleRun MuTect for a sample
run.post.processingrun.post.processing
run.target.qcPerform sample QC by looking at target coverage.
run.target.qc.sampleGet ontarget reads and run coverage quality control
run.vardict.samplerun.vardict.sample
run.variant.callingrun.variant.calling
run.varitas.pipelineRun VariTAS pipeline in full.
run.varitas.pipeline.hybridrun.varitas.pipeline.hybrid
run.varscan.sampleRun VarScan for a sample
save.configsave.config
save.coverage.excelSave coverage statistics to multi-worksheet Excel file.
save.variants.excelSave variants to Excel.
set.varitas.optionsSet options for varitas pipeline.
split.on.columnsplit.on.column
sum.dp4sum.dp4
system.lsRun ls command
tabular.meantabular.mean
tabular.mediantabular.median
trinucleotide.barplotMake barplot of trinucleotide substitutions
variant.recurrence.barplotMake barplot of variants per caller
variants.caller.barplotMake barplot of variants per caller
variants.sample.barplotMake barplot of variants per sample
verify.bam.specificationCheck that sample specification data frame matches expected...
verify.bwa.indexverify.bwa.index
verify.fasta.indexverify.fasta.index
verify.fastq.specificationCheck that FASTQ specification data frame matches expected...
verify.sequence.dictionaryverify.sequence.dictionary
verify.varitas.optionsCheck against common errors in the VariTAS options.
verify.vcf.specificationverify.vcf.specification
varitas documentation built on Feb. 21, 2020, 5:06 p.m.