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How to plot single gremlin CNV case sample against cohort mode in a figure?

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    Genevieve Brandt (she/her)

    Hi Faisal Almalki,

    I think you're on the right track! We also use the denoise copy ratio tsv files to make plots. I couldn't find any other scripts that our team uses. Potentially other users on this forum might have more insight!

    Thanks for the question,

    Genevieve

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    Faisal Almalki

    thank you Genevieve.

    That was helpful. 

    One more question. I dont have tsv format for

    denoisedCR
    --denoised-copy-ratios

    I believe its mandatory to plot the data. I got message after running GATK stats that LOG2_COPY_RATIO is missing.

    Do you know how to figure out this, please!!

    Regards

    Faisal

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    Genevieve Brandt (she/her)

    Could you share your full command and program log so that we can look into it more closely?

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    Faisal Almalki

    This is my command:

     

    ./gatk DenoiseReadCounts -I sampleinput.tsv --annotated-intervals intervallist.cohort.gc.filtered.annotated.tsv --denoised-copy-ratios sample_0_denoised_copy_ratios.tsv

     

    But I think I figure out my problem. Because I have germline sample, I do not have  panel of normals. 

    I need to follow this tutorial to figure out what I need to do. 

    https://gatk.broadinstitute.org/hc/en-us/articles/360041416032-DenoiseReadCounts

    "If no panel is provided, then the input counts are instead standardized by 1) transforming to fractional coverage, 2) performing optional explicit GC-bias correction (if GC-content annotated intervals are provided), 3) dividing by the sample median, and 4) transforming to log2 copy ratio. No denoising is performed, so the denoised result is simply taken to be identical to the standardized result."

    Things are clear now. 

    Thank you

    Faisal 

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    Genevieve Brandt (she/her)

    Okay great! Thanks for the update Faisal.

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