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 |