Variant Calling in Targeted Analysis Sequencing Data
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Documentation for package ‘varitas’ version 0.0.2
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 |