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Call Paired Somatic CNV

Dear All,

I'm planning to use Terra to run the paired somatic CNV workflow, but I'm not sure how this workflow calls somatic CNVs.
1. The wdl script calls CNVs for tumor, denoise tumor with PON, and plot segments;
2. Calls CNVs for the normal and, denoise tumor with PON, and plot segments;
Then, the workflow ends. I'm wondering how the workflow get rid of normal CNVs? Do I need to extract CNVs existing in normal from the somatic result manually?

It is very clear in Mutect2 that when running the command, I can also input -I normal for the program to extract normal mutations. Could you help me clarify the step where GATK remove normal CNVs?

In Mutect2

gatk --java-options "-Xmx${command_mem}m" Mutect2 \
    -R ${ref_fasta} \
    $tumor_command_line \
    $normal_command_line \
    ${"--germline-resource " + gnomad} \
    ${"-pon " + pon}

In DenoiseReadCounts

        gatk --java-options "-Xmx${command_mem_mb}m" DenoiseReadCounts \
            --input ${read_counts} \
            --count-panel-of-normals ${read_count_pon} \
            ${"--number-of-eigensamples " + number_of_eigensamples} \
            --standardized-copy-ratios ${entity_id}.standardizedCR.tsv \
            --denoised-copy-ratios ${entity_id}.denoisedCR.tsv

Thank you!

Best Answers


  • lzhan140lzhan140 Member

    Hi @bhanuGandham
    Thanks for your answer, we have already shared the space before. Our workspace is pd-wgs-project/pd-wgs-workspace/.

    There is no actual workflow for somatic CNV in our workspace now. We are just checking the demo workflow scripts at help-gatk/Somatic-CNVs-GATK4.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @lzhan140

    The tool creates a panel of normals that forms the baseline for what is the norm against which the workflow compares case samples. Take a look at this notebook tutorial on Terra that walks you through how CNV works in a very user friendly way

  • lzhan140lzhan140 Member

    Hi @slee,
    Thanks a lot for the answer. It solved my question. I have two additional questions regarding the PON:

    1. If I use different resources to create my PON, for example, a mix of depth 30x and 60x or WES and WGS. Will this confuse the program? Should I use just one type, like only 30x WGS or only 60x WES?

    2. If my PON is created by using a different depth of samples than my case samples, will the program know it? e.g. My PON is created by some 60x WGS but all my case samples are 30x WGS. Will the program know the difference and give me expected CNV calls or will it treat my case samples to be all deletions? since my case samples only have half the coverage than "Normals".


  • lzhan140lzhan140 Member

    @slee, thank you so much for the answer.

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