MSK-ACCESS Quality Control (QC) Version 1 (v1) is intended to ensure all samples are processed in an accurate and consistent manner using the https://github.com/mskcc/ACCESS-Pipeline workflow.
The following pages give descriptions on how to interpret Quality Control metrics presented in the PDF report, page by page.
Here is an example Quality Control report for the V1 ACCESS pipeline:
Note: All output sections in the following pages will refer to files found in the QC_Results folder from a V1 ACCESS pipeline run.
The subfolders are named as: waltz_<bam_type>_<pool_A_or_B>_(exon_level_files)?
There will be 12 such subfolders, and each will contain a copy of that metrics file, for the specific combination of bam type and Pool (which may be either target-specific or bait-specific) that is listed.