add.option	add.option
alternate.gene.sort	alternate.gene.sort
build.variant.specification	build.variant.specification
caller.overlap.venn.diagram	caller.overlap.venn.diagram
capitalise.caller	capitalize.caller
capitalize.caller	capitalize.caller
classify.variant	classify.variant
convert.ides.output	convert.ides.output
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
filter.variant.file	filter.variant.file
filter.variants	filter.variants
fix.lofreq.af	fix.lofreq.af
fix.names	fix.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	get.colours
get.coverage.by.amplicon	get.coverage.by.amplicon
get.coverage.by.sample.statistics	get.coverage.by.sample.statistics
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	get.option
get.panel.coverage.by.gene	get.panel.coverage.by.gene
get.pool.from.panel.data	get.pool.from.panel.data
get.varitas.options	get.varitas.options
get.vcf.chromosomes	get.vcf.chromosomes
in.varitas.options	in.varitas.options
logical.to.character	logical.to.character
make.command.line.call	make.command.line.call
mean.field.value	mean.field.value
merge.ides.annotation	merge.ides.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.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
prepare.bam.specification	prepare.bam.specification
prepare.fastq.specification	prepare.fastq.specification
prepare.miniseq.specifications	prepare.miniseq.specifications
prepare.vcf.specification	prepare.vcf.specification
process.coverage.reports	process.coverage.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.file
read.variant.calls	read.variant.calls
read.yaml	read.yaml
run.alignment	run.alignment
run.alignment.sample	run.alignment.sample
run.all.scripts	run.all.scripts
run.annotation	run.annotation
run.annovar.vcf	run.annovar.vcf
run.filtering.txt	run.filtering.txt
run.ides	run.ides
run.lofreq.sample	run.lofreq.sample
run.muse.sample	run.muse.sample
run.mutect.sample	run.mutect.sample
run.post.processing	run.post.processing
run.target.qc	run.target.qc
run.target.qc.sample	run.target.qc.sample
run.vardict.sample	run.vardict.sample
run.variant.calling	run.variant.calling
run.varitas.pipeline	run.varitas.pipeline
run.varitas.pipeline.hybrid	run.varitas.pipeline.hybrid
run.varscan.sample	run.varscan.sample
save.config	save.config
save.coverage.excel	save.coverage.excel
save.variants.excel	save.variants.excel
set.varitas.options	set.varitas.options
split.on.column	split.on.column
sum.dp4	sum.dp4
system.ls	system.ls
tabular.mean	tabular.mean
tabular.median	tabular.median
trinucleotide.barplot	trinucleotide.barplot
variant.recurrence.barplot	variant.recurrence.barplot
variants.caller.barplot	variants.caller.barplot
variants.sample.barplot	variants.sample.barplot
verify.bam.specification	verify.bam.specification
verify.bwa.index	verify.bwa.index
verify.fasta.index	verify.fasta.index
verify.fastq.specification	verify.fastq.specification
verify.sequence.dictionary	verify.sequence.dictionary
verify.varitas.options	verify.varitas.options
verify.vcf.specification	verify.vcf.specification
