Overview

This pipeline takes BAMs and runs selected Quality Control (QC) steps. Available algorithms are currently SAMtools stats, Picard CollectWgsMetrics, Picard CollectHsMetrics, FastQC, Qualimap bamqc, mosdepth coverage and mosdepth quantize. 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.

For DNA panels/targeted sequencing, intervals may be provided and will be used with CollectHsMetrics, mosdepth and Qualimap bamQC. CollectHsMetrics requires intervals and an optional bait file may also be provided.

---