R: Variant Calling in Targeted Analysis Sequencing Data

# Variant Calling in Targeted Analysis Sequencing Data

## Documentation for package ‘varitas’ version 0.0.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

add.option | add.option
alternate.gene.sort | alternate.gene.sort
build.variant.specification | build.variant.specification
caller.overlap.venn.diagram | . Make Venn diagram of variant caller overlap
capitalise.caller | capitalize.caller
capitalize.caller | capitalize.caller
classify.variant | classify.variant
convert.ides.output | Convert output of iDES step 1 to variant call format
create.directories | create.directories
date.stamp.file.name | date.stamp.file.name
datestamp.file.name | date.stamp.file.name
datestamp.filename | date.stamp.file.name
extract.sample.ids | Extract sample IDs from file paths
filter.variant.file | Filter variants in file.
filter.variants | Filter variant calls
fix.lofreq.af | fix.lofreq.af
fix.names | Fix variant call column names
fix.varscan.af | fix.varscan.af
get.base.substitution | Get base substitution
get.bed.chromosomes | get.bed.chromosomes
get.buildver | get.buildver
get.colours | Generate a colour scheme
get.coverage.by.amplicon | Process sample coverage per amplicon data
get.coverage.by.sample.statistics | Get statistics about coverage per sample
get.fasta.chromosomes | get.fasta.chromosomes
get.file.path | get.file.path
get.filters | get.filters
get.gene | get.gene
get.miniseq.sample.files | get.miniseq.sample.files
get.option | Helper function to recursively get an VariTAS option
get.panel.coverage.by.gene | Summarise panel coverage by gene
get.pool.from.panel.data | Get pool corresponding to each amplicon
get.varitas.options | Return VariTAS settings
get.vcf.chromosomes | get.vcf.chromosomes
in.varitas.options | Check if a key is in VariTAS options
logical.to.character | logical.to.character
make.command.line.call | Make string with command line call from its individual components
mean.field.value | mean.field.value
merge.ides.annotation | Merge potential iDES calls with variant annotation.
merge.variants | Merge variants
overwrite.varitas.options | overwrite.varitas.options
parse.job.dependencies | Parse job dependencies
plot.amplicon.coverage.per.sample | plot.amplicon.coverage.per.sample
plot.coverage.by.genome.order | Plot amplicon coverage by genome order
plot.coverage.by.sample | plot.coverage.by.sample
plot.ontarget.percent | plot.ontarget.percent
plot.paired.percent | plot.paired.percent
post.processing | Post-processing of variants to generate outputs
prepare.bam.specification | Prepare BAM specification data frame to standardized format for downstream analyses.
prepare.fastq.specification | prepare.fastq.specification
prepare.miniseq.specifications | prepare.miniseq.specifications
prepare.vcf.specification | prepare.vcf.specification
process.coverage.reports | Process coverageBed reports
process.sample.contamination.checks | Process sample contamination checks
process.total.coverage.statistics | Process total coverage statistics
read.all.calls | read.all.calls
read.ides.file | Read iDES output
read.variant.calls | Read variant calls from file and format for ease of downstream analyses.
read.yaml | read.yaml
run.alignment | Run alignment
run.alignment.sample | Run alignment for a single sample
run.all.scripts | Run all the generated bash scripts without HPC commands
run.annotation | Run annotation on a set of VCF files
run.annovar.vcf | Run ANNOVAR on a VCF file
run.filtering.txt | Run filtering on an ANNOVAR-annotated txt file
run.ides | Run iDES
run.lofreq.sample | Run LoFreq for a sample
run.muse.sample | Run MuSE for a sample
run.mutect.sample | Run MuTect for a sample
run.post.processing | run.post.processing
run.target.qc | Perform sample QC by looking at target coverage.
run.target.qc.sample | Get ontarget reads and run coverage quality control
run.vardict.sample | run.vardict.sample
run.variant.calling | run.variant.calling
run.varitas.pipeline | Run VariTAS pipeline in full.
run.varitas.pipeline.hybrid | run.varitas.pipeline.hybrid
run.varscan.sample | Run VarScan for a sample
save.config | save.config
save.coverage.excel | Save coverage statistics to multi-worksheet Excel file.
save.variants.excel | Save variants to Excel.
set.varitas.options | Set options for varitas pipeline.
split.on.column | split.on.column
sum.dp4 | sum.dp4
system.ls | Run ls command
tabular.mean | tabular.mean
tabular.median | tabular.median
trinucleotide.barplot | Make barplot of trinucleotide substitutions
variant.recurrence.barplot | Make barplot of variants per caller
variants.caller.barplot | Make barplot of variants per caller
variants.sample.barplot | Make barplot of variants per sample
verify.bam.specification | Check that sample specification data frame matches expected format, and that all files exist
verify.bwa.index | verify.bwa.index
verify.fasta.index | verify.fasta.index
verify.fastq.specification | Check that FASTQ specification data frame matches expected format, and that all files exist
verify.sequence.dictionary | verify.sequence.dictionary
verify.varitas.options | Check against common errors in the VariTAS options.
verify.vcf.specification | verify.vcf.specification