Variant Calling in Targeted Analysis Sequencing Data
Run alignment for a single sample
Run all the generated bash scripts without HPC commands
add.option
alternate.gene.sort
build.variant.specification
. Make Venn diagram of variant caller overlap
capitalize.caller
classify.variant
Convert output of iDES step 1 to variant call format
create.directories
date.stamp.file.name
Extract sample IDs from file paths
Filter variants in file.
Filter variant calls
fix.lofreq.af
Fix variant call column names
fix.varscan.af
Get base substitution
get.bed.chromosomes
get.buildver
Generate a colour scheme
Process sample coverage per amplicon data
Get statistics about coverage per sample
get.fasta.chromosomes
get.file.path
get.filters
get.gene
get.miniseq.sample.files
Helper function to recursively get an VariTAS option
Summarise panel coverage by gene
Get pool corresponding to each amplicon
Return VariTAS settings
get.vcf.chromosomes
Check if a key is in VariTAS options
logical.to.character
Make string with command line call from its individual components
mean.field.value
Merge potential iDES calls with variant annotation.
Merge variants
overwrite.varitas.options
Parse job dependencies
plot.amplicon.coverage.per.sample
Plot amplicon coverage by genome order
plot.coverage.by.sample
plot.ontarget.percent
plot.paired.percent
Post-processing of variants to generate outputs
Prepare BAM specification data frame to standardized format for downst...
prepare.fastq.specification
prepare.miniseq.specifications
prepare.vcf.specification
Process coverageBed reports
Process sample contamination checks
Process total coverage statistics
read.all.calls
Read iDES output
Read variant calls from file and format for ease of downstream analyse...
read.yaml
Run alignment
Run annotation on a set of VCF files
Run ANNOVAR on a VCF file
Run filtering on an ANNOVAR-annotated txt file
Run iDES
Run LoFreq for a sample
Run MuSE for a sample
Run MuTect for a sample
run.post.processing
Perform sample QC by looking at target coverage.
Get ontarget reads and run coverage quality control
run.vardict.sample
run.variant.calling
run.varitas.pipeline.hybrid
Run VariTAS pipeline in full.
Run VarScan for a sample
save.config
Save coverage statistics to multi-worksheet Excel file.
Save variants to Excel.
Set options for varitas pipeline.
split.on.column
sum.dp4
Run ls command
tabular.mean
tabular.median
Make barplot of trinucleotide substitutions
Make barplot of variants per caller
Make barplot of variants per caller
Make barplot of variants per sample
Check that sample specification data frame matches expected format, an...
verify.bwa.index
verify.fasta.index
Check that FASTQ specification data frame matches expected format, and...
verify.sequence.dictionary
Check against common errors in the VariTAS options.
verify.vcf.specification
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.