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varitas (version 0.0.2)

Variant Calling in Targeted Analysis Sequencing Data

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.

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Version

Install

install.packages('varitas')

Monthly Downloads

179

Version

0.0.2

License

GPL-2

Maintainer

Adam Mills

Last Published

November 14th, 2020

Functions in varitas (0.0.2)

capitalize.caller

capitalize.caller
create.directories

create.directories
alternate.gene.sort

alternate.gene.sort
classify.variant

classify.variant
extract.sample.ids

Extract sample IDs from file paths
convert.ides.output

Convert output of iDES step 1 to variant call format
date.stamp.file.name

date.stamp.file.name
add.option

add.option
build.variant.specification

build.variant.specification
get.bed.chromosomes

get.bed.chromosomes
fix.varscan.af

fix.varscan.af
get.base.substitution

Get base substitution
read.ides.file

Read iDES output
get.coverage.by.sample.statistics

Get statistics about coverage per sample
get.pool.from.panel.data

Get pool corresponding to each amplicon
fix.names

Fix variant call column names
get.varitas.options

Return VariTAS settings
fix.lofreq.af

fix.lofreq.af
plot.paired.percent

plot.paired.percent
filter.variant.file

Filter variants in file.
get.panel.coverage.by.gene

Summarise panel coverage by gene
get.option

Helper function to recursively get an VariTAS option
caller.overlap.venn.diagram

. Make Venn diagram of variant caller overlap
get.buildver

get.buildver
verify.vcf.specification

verify.vcf.specification
merge.variants

Merge variants
parse.job.dependencies

Parse job dependencies
overwrite.varitas.options

overwrite.varitas.options
get.colours

Generate a colour scheme
get.fasta.chromosomes

get.fasta.chromosomes
process.coverage.reports

Process coverageBed reports
prepare.vcf.specification

prepare.vcf.specification
mean.field.value

mean.field.value
merge.ides.annotation

Merge potential iDES calls with variant annotation.
plot.ontarget.percent

plot.ontarget.percent
get.gene

get.gene
filter.variants

Filter variant calls
read.all.calls

read.all.calls
get.coverage.by.amplicon

Process sample coverage per amplicon data
prepare.fastq.specification

prepare.fastq.specification
process.sample.contamination.checks

Process sample contamination checks
prepare.miniseq.specifications

prepare.miniseq.specifications
split.on.column

split.on.column
run.annovar.vcf

Run ANNOVAR on a VCF file
variants.sample.barplot

Make barplot of variants per sample
plot.amplicon.coverage.per.sample

plot.amplicon.coverage.per.sample
system.ls

Run ls command
process.total.coverage.statistics

Process total coverage statistics
run.varscan.sample

Run VarScan for a sample
logical.to.character

logical.to.character
get.file.path

get.file.path
plot.coverage.by.genome.order

Plot amplicon coverage by genome order
plot.coverage.by.sample

plot.coverage.by.sample
tabular.mean

tabular.mean
run.post.processing

run.post.processing
get.vcf.chromosomes

get.vcf.chromosomes
in.varitas.options

Check if a key is in VariTAS options
get.filters

get.filters
run.target.qc

Perform sample QC by looking at target coverage.
variants.caller.barplot

Make barplot of variants per caller
run.all.scripts

Run all the generated bash scripts without HPC commands
get.miniseq.sample.files

get.miniseq.sample.files
read.variant.calls

Read variant calls from file and format for ease of downstream analyses.
set.varitas.options

Set options for varitas pipeline.
make.command.line.call

Make string with command line call from its individual components
verify.varitas.options

Check against common errors in the VariTAS options.
run.alignment.sample

Run alignment for a single sample
run.alignment

Run alignment
run.lofreq.sample

Run LoFreq for a sample
run.filtering.txt

Run filtering on an ANNOVAR-annotated txt file
post.processing

Post-processing of variants to generate outputs
run.ides

Run iDES
verify.fastq.specification

Check that FASTQ specification data frame matches expected format, and that all files exist
save.config

save.config
run.varitas.pipeline.hybrid

run.varitas.pipeline.hybrid
run.vardict.sample

run.vardict.sample
prepare.bam.specification

Prepare BAM specification data frame to standardized format for downstream analyses.
read.yaml

read.yaml
verify.bwa.index

verify.bwa.index
run.varitas.pipeline

Run VariTAS pipeline in full.
verify.sequence.dictionary

verify.sequence.dictionary
run.target.qc.sample

Get ontarget reads and run coverage quality control
verify.bam.specification

Check that sample specification data frame matches expected format, and that all files exist
save.coverage.excel

Save coverage statistics to multi-worksheet Excel file.
run.muse.sample

Run MuSE for a sample
run.annotation

Run annotation on a set of VCF files
verify.fasta.index

verify.fasta.index
run.mutect.sample

Run MuTect for a sample
run.variant.calling

run.variant.calling
save.variants.excel

Save variants to Excel.
variant.recurrence.barplot

Make barplot of variants per caller
tabular.median

tabular.median
trinucleotide.barplot

Make barplot of trinucleotide substitutions
sum.dp4

sum.dp4