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 |
