README.md
In cgab-ncc/FIREVAT: FIREVAT, FInding REliable Variants without ArTifacts

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.

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)

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")

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

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