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

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Faisal Almalki

• October 28, 2021 12:32

Basically I followed this tutorial for calling germline CNV from whole exome data set. https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants

First, I have generated a cohort mode. Then, I have call CNV for a sample against the cohort. 

I end up with two vcf files interval genotype, segment genotype. Also I have a denoise copy ratio as a tsv fromat for the sample. 

Looking for del and dup for each interval or each segment is not convenient from vcf. This is because VCF file provides a detailed listing of the most likely copy-number call for each genomic interval included in the data set. 

My query is how to visualise data in a figure. Should I plot denoise copy ratio as y axis against coordinate x axis? Or Should I used interval CN as y axis?

Regards

Faisal

 

 

 

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  Genevieve Brandt (she/her)

  • December 20, 2021 17:57

  Okay great! Thanks for the update Faisal.

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  Genevieve Brandt (she/her)

  • December 07, 2021 20:11

  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

  • December 14, 2021 13:43
  • Edited

  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)

  • December 17, 2021 04:35

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

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  Faisal Almalki

  • December 19, 2021 17:14

  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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