API for varitas
Variant Calling in Targeted Analysis Sequencing Data

Global functions
.onLoad Source code
add.option Man page Source code
alternate.gene.sort Man page Source code
build.variant.specification Man page Source code
caller.overlap.venn.diagram Man page Source code
capitalise.caller Man page
capitalize.caller Man page Source code
classify.variant Man page Source code
convert.ides.output Man page Source code
create.directories Man page Source code
date.stamp.file.name Man page
datestamp.file.name Man page
datestamp.filename Man page Source code
extract.sample.ids Man page Source code
filter.variant.file Man page Source code
filter.variants Man page Source code
fix.lofreq.af Man page Source code
fix.names Man page Source code
fix.varscan.af Man page Source code
get.base.substitution Man page Source code
get.bed.chromosomes Man page Source code
get.buildver Man page Source code
get.colours Man page Source code
get.coverage.by.amplicon Man page Source code
get.coverage.by.sample.statistics Man page Source code
get.fasta.chromosomes Man page Source code
get.file.path Man page Source code
get.filters Man page Source code
get.gene Man page Source code
get.miniseq.sample.files Man page Source code
get.option Man page Source code
get.panel.coverage.by.gene Man page Source code
get.pool.from.panel.data Man page Source code
get.varitas.options Man page Source code
get.vcf.chromosomes Man page Source code
in.varitas.options Man page Source code
logical.to.character Man page Source code
make.command.line.call Man page Source code
mean.field.value Man page Source code
merge.ides.annotation Man page Source code
merge.variants Man page Source code
overwrite.varitas.options Man page Source code
parse.job.dependencies Man page Source code
plot.amplicon.coverage.per.sample Man page Source code
plot.coverage.by.genome.order Man page Source code
plot.coverage.by.sample Man page Source code
plot.ontarget.percent Man page Source code
plot.paired.percent Man page Source code
post.processing Man page Source code
prepare.bam.specification Man page Source code
prepare.fastq.specification Man page Source code
prepare.miniseq.specifications Man page Source code
prepare.vcf.specification Man page Source code
process.coverage.reports Man page Source code
process.sample.contamination.checks Man page Source code
process.total.coverage.statistics Man page Source code
read.all.calls Man page Source code
read.ides.file Man page Source code
read.variant.calls Man page Source code
read.yaml Man page Source code
run.alignment Man page Source code
run.alignment.sample Man page Source code
run.all.scripts Man page Source code
run.annotation Man page Source code
run.annovar.vcf Man page Source code
run.filtering.txt Man page Source code
run.ides Man page Source code
run.lofreq.sample Man page Source code
run.muse.sample Man page Source code
run.mutect.sample Man page Source code
run.post.processing Man page Source code
run.target.qc Man page Source code
run.target.qc.sample Man page Source code
run.vardict.sample Man page Source code
run.variant.calling Man page Source code
run.varitas.pipeline Man page Source code
run.varitas.pipeline.hybrid Man page Source code
run.varscan.sample Man page Source code
save.config Man page Source code
save.coverage.excel Man page Source code
save.variants.excel Man page Source code
set.varitas.options Man page Source code
split.on.column Man page Source code
sum.dp4 Man page Source code
system.ls Man page Source code
tabular.mean Man page Source code
tabular.median Man page Source code
trinucleotide.barplot Man page Source code
variant.recurrence.barplot Man page Source code
variants.caller.barplot Man page Source code
variants.sample.barplot Man page Source code
verify.bam.specification Man page Source code
verify.bwa.index Man page Source code
verify.fasta.index Man page Source code
verify.fastq.specification Man page Source code
verify.sequence.dictionary Man page Source code
verify.varitas.options Man page Source code
verify.vcf.specification Man page Source code
varitas documentation built on Feb. 21, 2020, 5:06 p.m.