tmp/museCalling.R

In msubirana/ergWgsTools: What the Package Does (One Line, Title Case)

source('/imppc/labs/lplab/share/marc/repos/ergWgsTools/tmp/variables.R')
library(devtools)
devtools::load_all('/imppc/labs/lplab/share/marc/repos/ergWgsTools')
threads <- parallel::detectCores()

# check BAM indexes
sambambaIndex(bam = tumor_file,
              threads = threads)

sambambaIndex(bam = normal_file,
              threads = threads)

# MuSE calling
museCalling(tumor_file = tumor_file,
            normal_file = normal_file,
            sample_name = sample_name,
            ref = ref,
            out_path = out_path,
            muse = muse,
            af_only_gnomad = af_only_gnomad,
            bcftools = bcftools)