FIREVAT

FIREVAT (FInding REliable Variants without ArTifacts) is an R package that performs variant refinement on cancer sequencing data. FIREVAT uses mutational signatures to identify sequencing artifacts and low-quality variants.

Getting started

Installation

To install the developmental version of FIREVAT from GitHub:

install.packages("devtools")
devtools::install_github("cgab-ncc/FIREVAT", dependencies = TRUE)

FIREVAT depends on the following packages

• BSgenome.Hsapiens.UCSC.hg19
• BSgenome.Hsapiens.UCSC.hg38
• rngtools

To install the above packages:

install.packages("BiocManager")
# The default input genome for FIREVAT is human genomes (hg19, hg38)
BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")
# If you want to apply FIREVAT to another species, you can use other BSgenomes
# ex) mm10
BiocManager::install("BSgenome.Mmusculus.UCSC.mm10")



# If you are using R < 3.6.0
package.url <- "http://cran.r-project.org/src/contrib/Archive/rngtools/rngtools_1.3.1.tar.gz"
devtools::install_url(url = package.url, dependencies = TRUE)

# If you are using R >= 3.6.0
install.packages("rngtools")

If you are a Windows user, please install Rtools first.

To install the released FIREVAT version:

install.packages("devtools")
devtools::install_local("/path/to/FIREVAT_<version>.tar.gz", dependencies = TRUE)

Usage

FIREVAT accepts a Variant Call Format (VCF) file as the primary input. It also requires a configuration (JSON) file that corresponds to the attributes found in the VCF file. The variant refinement is then performed by running the following code example:

library(FIREVAT)

# Output directory
output.dir <- "" # assign this path

# VCF file
sample.vcf.file <- system.file("extdata", "DCC_PCAWG_Cell_Lines_HCC1954.vcf", package = "FIREVAT")

# Configuration file
config.file <- system.file("config", "PCAWG_DKFZ_Cell_Line_Filtering_Params.json", package = "FIREVAT")

# Run FIREVAT
results <- RunFIREVAT(vcf.file = sample.vcf.file,
                      vcf.file.genome = 'hg19', # for mouse variants: 'mm10'
                      config.file = config.file,
                      df.ref.mut.sigs = GetPCAWGMutSigs(),
                      target.mut.sigs = GetPCAWGMutSigsNames(),
                      sequencing.artifact.mut.sigs = PCAWG.All.Sequencing.Artifact.Signatures,
                      output.dir = output.dir,
                      objective.fn = Default.Obj.Fn,
                      num.cores = 2,
                      ga.pop.size = 100,
                      ga.max.iter = 5,
                      ga.run = 5,
                      perform.strand.bias.analysis = TRUE,
                      ref.forward.strand.var = "TumorDPRefForward",
                      ref.reverse.strand.var = "TumorDPRefReverse",
                      alt.forward.strand.var = "TumorDPAltForward",
                      alt.reverse.strand.var = "TumorDPAltReverse",
                      annotate = FALSE)

Running the code above will generate FIREVAT outputs, including HTML report, refined.vcf, and artifact.vcf files:

Feel free to take a look at the sample HTML report. The sample FIREVAT output files (zipped ) are available here.

For your convenience, we have prepared configuration (JSON) files for popularly used variant callers:

# MuTect2
mutect2.config.file <- system.file("config", "MuTect2_Filtering_Params.json", package = "FIREVAT")

# Muse
muse.config.file <- system.file("config", "Muse_Filtering_Params.json", package = "FIREVAT")

# SomaticSniper
somaticsniper.config.file <- system.file("config", "SomaticSniper_Filtering_Params.json", package = "FIREVAT")

# Varscan2
varscan2.config.file <- system.file("config", "Varscan2_Filtering_Params.json", package = "FIREVAT")

# Strelka
strelka.config.file <- system.file("config", "Strelka_Filtering_Params.json", package = "FIREVAT")

Vignette

In Introduction to FIREVAT, you can find advanced examples and detailed tutorials on how to use FIREVAT.

Suggested workflow

Based on our validation studies, we suggest using FIREVAT in the following workflow:

Paper

Kim, H., Lee, A.J., Lee, J. et al. FIREVAT: finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures. Genome Med 11, 81 (2019) doi:10.1186/s13073-019-0695-x

Authors

• Andy Jinseok Lee, Bioinformatics Analysis Team, National Cancer Center Korea.
• Hyunbin Kim, Bioinformatics Analysis Team, National Cancer Center Korea.

Attributions

FIREVAT is developed and maintained by Andy Jinseok Lee ([email protected]) and Hyunbin Kim ([email protected]).

License

MIT License