data-raw/production_scripts/PCAWG_collaboratory_set2.R

In steverozen/DBSverify: Analyze Next Generation Sequencing Data to Verify Somatic Double-BaseSubstituion (DBS) Calls

#!/usr/local/bin/Rscript

library(DBSverify)

PCAWG_read_table_and_evaluate_DBS(
  in.table = "~/DBSverify/data-raw/production_scripts/collaboratory_bams_2021_07_16.csv",
  in.vcf.dir  = "~/mvv/PCAWG_all_Collaboratory_VCFs_and_BEDs/",
  minibam.dir = "~/mvv/collab-minibams-set2/",
  out.vcf.dir = "~/mvv/collab-minibams-set2-output-VCFs/")

# Just in case options(warn = 1) didn't work
warnings()