tmp/pindelCalling.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)

# Pindel calling
pindelCalling(tumor_file = tumor_file,
              normal_file = normal_file,
              sample_name = sample_name,
              ref = ref,
              out_path = out_path,
              pindel = pindel,
              sambamba = sambamba,
              samtools = samtools,
              threads = threads,
              perl = perl,
              gatk4 = gatk4,
              centromeres_telomeres = centromeres_telomeres,
              bcftools = bcftools)