@zwdzwd Not sure how you want to handle the README, but I've committed some changes and wanted to keep the two versions in line.
Changes:
README - formatting and changing references to huishenlab
Preparing to deprecate biscuit markdup in preference of using the biscuitBlaster pipeline
Removing reference to -x option in biscuit align until further testing can be done (-x still works if used, but it hasn't been tested so the help message has been removed until fully verified)
Updating biscuit pileup somatic mode with new flags to specify tumor and normal bams
Updates to QC script - I plan to go through and do a better job of revamping this in the near future
@zwdzwd Not sure how you want to handle the README, but I've committed some changes and wanted to keep the two versions in line.
Changes: