Description Usage Arguments Value
Run the BATCAVE algorithm
1 2 3 | run_batcave(vcf, reference, file_type = "vcf", seq_type = "wgs",
sample_name = "TUMOR", min_vaf = 0.05, min_odds = 10,
plot_path = NULL, profile_path = NULL)
|
vcf |
Output of MuTect 1.1.7 (call stats) or 2.0 (VCF 4.0). |
reference |
The genome reference used for alignment and variant calling (BSgenome Object) |
file_type |
The file type of "vcf" (default = "vcf") |
seq_type |
The type of sequencing experiment. Whole Genome "wgs" or Whole Exome "wes" (default = "wgs") |
sample_name |
The name of the tumor sample (default = "TUMOR") |
min_vaf |
The minimum allele frequency to use to compute mutation rate per base (default = "0.05) |
min_odds |
The odds ratio cutoff for high-confidence mutations used to compute prior probability of mutation (default = "10" which corresponds to MuTect TLOD = 7.3) |
plot_path |
The file name to use for a plot of the empirical mutation profile (default = "NULL" for no plot) |
profile_path |
The file name to use for a tab separated file containing the empirical mutation profile (default = "NULL" for no file) |
a data frame with 11 columns: chrom
the chromosome the variant is on,
start
and end
the position of the variant, ref
and alt
the reference and alternate alleles,
context
the tri-nucleotide context of the variant, TLOD
the score reported by MuTect, freq
the variant allele frequency,
pass_all
a boolean column that is TRUE is the variant passed all MuTect filters and FALSE otherwise,
tlod_only
a boolean column that is TRUE is the variant passed all MuTect filters except the TLOD filter and false otherwise,
pprob_variant
the posterior probability for the variant computed using the BATCAVE algorithm
@examples ## Not run: ## input files and varianbles 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) ## End(Not run)
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