batcaver - BATCAVE: Calling somatic mutations with a tumor-and-site-specific prior
This package is an implementation of the BATCAVE algorithm described in Mannakee et al. ....
The algorithm is a post-variant-calling filter for variants that incorporates a tumor-and-site-specific prior probability of mutation.
batcaver depends on several bioconductor packages for bam file manipulation as well as functions included in the tidyverse. The dependencies can be installed prior to installation of batcaver using the following commands.
### Not run
## install dependencies
dependencies <- c("dplyr","tidyr","readr","magrittr","deconstructSigs","ggplot2","tictoc","crayon","glue","devtools")
install.packages(dependencies)
source("https://bioconductor.org/biocLite.R")
biocLite(c("Rsamtools","SomaticSignatures","GenomicAlignments","VariantAnnotation"))
## install batcaver
devtools::install_github("bmannakee/batcaver",build_vignettes=TRUE)
The algorithm takes as input a MuTect output file in either VCF 4.0 or call_stats format.
The package exports one main function run_batcave() (See function documentation) as well as the load_variants (see function documentation) function which is exported to facilitate trouble-shooting of the parsing of variant file formats.
Example code for run_batcave()
### not run
## input files and variables
#' library(BSgenome.Hsapiens.UCSC.hg38) # the BSgenome reference
#' vcf <- /path/to/MuTect/vcf
#' reference <- BSgenome.Hsapiens.UCSC.hg38
#' file_type <- "vcf"
#' seq_type <- "wes"
#' sample_name <- "TUMOR"
#' min_vaf <- .1
#' min_odds <- 10
#' plot_path <- /path/to/empirical/profile/plot.pdf
#' profile_path <- /path/to/empirical/profile/profile.tsv
#' fr <- run_batcave(vcf = vcf, reference = reference, file_type = file_type,
#' seq_type = seq_type, sample_name = sample_name, min_vaf = min_vaf,
#' min_odds = min_odds, plot_path = plot_path, profile_path = profile_path)
#' }