Overview

This pipeline takes BAMs and runs selected Quality Control (QC) steps. Available algorithms are currently SAMtools stats, Picard CollectWgsMetrics and Qualimap bamqc. Generally either Qualimap bamqc or SAMtools stats and Picard CollectWgsMetrics should be run, not both. Qualimap bamqc uses a lot of memory and should not be run within uclahs-cds/metapipeline-DNA. Input can include any combination of tumor and normal BAMs from a single donor. Each will be processed independently. RNA specific QC is not yet implemented but is expected soon.

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