Skip to content


BJ-CNV is a modified version of Ginkgo for copy number call. The pipeline takes deduplicated bam file, calculates coverage, performs normalization, and make cnv calls. Pipeline generates various plots and creates a table with copy number information with genomic coordinates. The CNV Tertiary pipeline is dependent on the secondary BJ-DNA-QC pipeline. Once the BJ-DNA-QC pipeline completes successfully, the prerequisites are met to launch the BJ-CNV pipeline.

Pipeline Overview#

flowchart LR
%% Colors %%
classDef panel fill:transparent,stroke:#323232,stroke-dasharray:8
classDef black fill:#12294C,stroke:#12294C,stroke-width:2px,color:#fff
classDef blue fill:#20A4F3,stroke:#20A4F3,stroke-width:2px,color:#fff
classDef green fill:#3BCEAC,stroke:#3BCEAC,stroke-width:2px,color:#fff
classDef yellow fill:#ffd166,stroke:#ffd166,stroke-width:2px,color:#fff
classDef pink fill:#ef476f,stroke:#ef476f,stroke-width:2px,color:#fff
classDef orange fill:#f3722c,stroke:#f3722c,stroke-width:2px,color:#fff
classDef red fill:#BB4430,stroke:#BB4430,stroke-width:2px,color:#fff
classDef ming fill:#387780,stroke:#387780,stroke-width:2px,color:#fff
    Start((Start)):::black --bam--> Coverage[Coverage]:::green
    subgraph Ginkgo
        Coverage --> QC:::green
        QC --> Remove-outliers:::green
        Remove-outliers --> Segment-bins:::green
        Segment-bins --> CNV-calls:::green
    subgraph Visualization-App
        CNV-calls --> report[CNV App]:::orange

    CNV-calls --> End((End)):::black

Following are the steps and tools that pipeline users to perform the analyses:

  • Convert BAM input files into BED files using bamtobed command from bedtools
  • Map the BED coverage files into prior computed bins using Ginkgo module
  • Perform segmentation, ploidy estimation, and create CNV plots using the Ginkgo module
  • Perform final CNV call using the Ginkgo module


Module Parameter Name Options Description
Ginkgo (default) CNV module evaluates the copy number using Ginkgo tool.
CNV (default) CNV module evaluates the copy number.
Bin Size (bp) 1000000 (default) Genomic bin size in bp to use for CNV.
Minimum Ploidy 1
1.5 (default)
Minimum Ploidy to set for calling CNV.
For haploid genome set to 1
Maximum Ploidy 6 (default) Maximum Ploidy to set for calling CNV.

Output files#

Output Directory/File
This section includes output files for the Copy Number Variant (CNV) data and information about the gains and losses for each biosample.

CNV profile example