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
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
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
