# A NGS analysis pipeline.

## Documentation for package ‘HTSeqGenie’ version 4.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

analyzeVariants | Calculate and process Variants
annotateVariants | Annotate variants via vep
buildGenomicFeaturesFromTxDb | Build genomic features from a TxDb object
callVariantsGATK | Variant calling via GATK
checkGATKJar | Check for the GATK jar file
detectRRNA | Detect rRNA Contamination in Reads
excludeVariantsByRegions | Filter variants by regions
gatk | gatk
generateSingleGeneDERs | generateSingleGeneDERs
getRRNAIds | Detect reads that look like rRNA
getTabDataFromFile | Load tabular data from the NGS pipeline result directory
hashCoverage | Hashing function for coverage
hashVariants | Hashing function for variants
hashVector | Hashing function for vector
HTSeqGenie | Package overview
isSparse | isSparse
markDuplicates | markDuplicates
markDups | markDups
realignIndels | realignIndels
realignIndelsGATK | Realign indels via GATK
runPipeline | Run the NGS analysis pipeline
runPipelineConfig | Run the NGS analysis pipeline
setupTestFramework | setup test framework
TP53GenomicFeatures | Demo genomic features around the TP53 gene
vcfStat | Compute stats on a VCF file
wrap.callVariants | Variant calling
writeVCF | writeVCF