#' run smartcallr.
#' Stub here
#' vcf is a mutect vcf 4.0 file
#' reference needs to be a FAFile object
#' vr <- smartcallr::compute_odds('./data/non_pdx/vcfs/AZ1013T1.vcf',reference=BSgenome.Hsapiens.1000genomes.hs37d5)
compute_odds <- function(vcf,reference,sample_name='TUMOR',prior_lod=5.0){
if (!file.exists(vcf)){
stop('The VCF path is not valid.')
}
# load the vcf as vranges
# Rules applied are filters for SNV and sample name
vars <- load_variants(vcf,reference,sample_name)
vars <- .compute_priors(vars,reference,prior_lod)
vars
}
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