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varitas  

Variant Calling in Targeted Analysis Sequencing Data
View on CRAN: Click here


Download and install varitas package within the R console
Install from CRAN:
install.packages("varitas")

Install from Github:
library("remotes")
install_github("cran/varitas")

Install by package version:
library("remotes")
install_version("varitas", "0.0.2")



Attach the package and use:
library("varitas")
Maintained by
Adam Mills
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-02-21
Latest Update: 2020-11-14
Description:
Multi-caller variant analysis pipeline for targeted analysis sequencing (TAS) data. Features a modular, automated workflow that can start with raw reads and produces a user-friendly PDF summary and a spreadsheet containing consensus variant information.
How to cite:
Adam Mills (2020). varitas: Variant Calling in Targeted Analysis Sequencing Data. R package version 0.0.2, https://cran.r-project.org/web/packages/varitas. Accessed 22 Dec. 2024.
Previous versions and publish date:
0.0.1 (2020-02-21 13:00)
Other packages that cited varitas R package
View varitas citation profile
Other R packages that varitas depends, imports, suggests or enhances
Complete documentation for varitas
Functions, R codes and Examples using the varitas R package
Some associated functions: add.option . alternate.gene.sort . build.variant.specification . caller.overlap.venn.diagram . capitalize.caller . classify.variant . convert.ides.output . create.directories . date.stamp.file.name . extract.sample.ids . filter.variant.file . filter.variants . fix.lofreq.af . fix.names . fix.varscan.af . get.base.substitution . get.bed.chromosomes . get.buildver . get.colours . get.coverage.by.amplicon . get.coverage.by.sample.statistics . get.fasta.chromosomes . get.file.path . get.filters . get.gene . get.miniseq.sample.files . get.option . get.panel.coverage.by.gene . get.pool.from.panel.data . get.varitas.options . get.vcf.chromosomes . in.varitas.options . logical.to.character . make.command.line.call . mean.field.value . merge.ides.annotation . merge.variants . overwrite.varitas.options . parse.job.dependencies . plot.amplicon.coverage.per.sample . plot.coverage.by.genome.order . plot.coverage.by.sample . plot.ontarget.percent . plot.paired.percent . post.processing . prepare.bam.specification . prepare.fastq.specification . prepare.miniseq.specifications . prepare.vcf.specification . process.coverage.reports . process.sample.contamination.checks . process.total.coverage.statistics . read.all.calls . read.ides.file . read.variant.calls . read.yaml . run.alignment . run.alignment.sample . run.all.scripts . run.annotation . run.annovar.vcf . run.filtering.txt . run.ides . run.lofreq.sample . run.muse.sample . run.mutect.sample . run.post.processing . run.target.qc . run.target.qc.sample . run.vardict.sample . run.variant.calling . run.varitas.pipeline.hybrid . run.varitas.pipeline . run.varscan.sample . save.config . save.coverage.excel . save.variants.excel . set.varitas.options . split.on.column . sum.dp4 . system.ls . tabular.mean . tabular.median . trinucleotide.barplot . variant.recurrence.barplot . variants.caller.barplot . variants.sample.barplot . verify.bam.specification . verify.bwa.index . verify.fasta.index . verify.fastq.specification . verify.sequence.dictionary . verify.varitas.options . verify.vcf.specification . 
Some associated R codes: add.option.R . caller.overlap.venn.diagram.R . convert.ides.output.R . filter.variant.file.R . filter.variants.R . fix.names.R . get.coverage.by.amplicon.R . get.coverage.by.sample.statistics.R . get.filters.R . get.gene.R . get.miniseq.sample.files.R . get.option.R . get.varitas.options.R . helper_functions.R . in.varitas.options.R . merge.variants.R . overwrite.varitas.options.R . plot.amplicon.coverage.per.sample.R . plot.coverage.by.genome.order.R . plot.coverage.by.sample.R . plot.ontarget.percent.R . plot.paired.percent.R . post.processing.R . prepare.bam.specification.R . prepare.fastq.specification.R . prepare.miniseq.specifications.R . prepare.vcf.specification.R . process.coverage.reports.R . process.sample.contamination.checks.R . process.total.coverage.statistics.R . read.all.calls.R . read.ides.file.R . read.variant.calls.R . run.alignment.R . run.alignment.sample.R . run.all.scripts.R . run.annotation.R . run.annovar.vcf.R . run.filtering.txt.R . run.ides.R . run.lofreq.sample.R . run.muse.sample.R . run.mutect.sample.R . run.post.processing.R . run.target.qc.R . run.target.qc.sample.R . run.vardict.sample.R . run.variant.calling.R . run.varitas.pipeline.R . run.varitas.pipeline.hybrid.R . run.varscan.sample.R . save.coverage.excel.R . save.variants.excel.R . set.varitas.options.R . setup.R . trinucleotide.barplot.R . variant.recurrence.barplot.R . variants.caller.barplot.R . variants.sample.barplot.R . varitas-pkg.R . verify.bam.specification.R . verify.bwa.index.R . verify.fasta.index.R . verify.fastq.specification.R . verify.sequence.dictionary.R . verify.varitas.options.R . verify.vcf.specification.R .  Full varitas package functions and examples
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