Difference between GATK Germline CNV Pipeline vs Genome STRiP?
Answered
My dataset contains 400 individuals and I have to find CNVs. Which pipeline I should use GATK or Genome STRiP? More important is that how both these programs are different from each other?
I am new to bioinformatic analysis however, I already had used GATK Germline Short Variant Discovery Pipeline and it was a good experience.
Looking forward to hear from experts soon.
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Bob Handsaker can provide insight about GenomeSTRiP.
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Dear Brandt, Thank you for referral. Can you please tell me if using GATK I may get absolute copy numbers?
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Compared to other methods, I would say that Genome STRiP is particularly good at utilizing normalized depth-of-coverage and multi-allelic CNVs that can be best detected based on this. The LCNV pipeline is also rather unique in trying to assess large, potentially mosaic CNVs from read depth, although tools like mocha are generally better powered.
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Hi Muhammad Shoaib Akhtar, the denoised copy ratio with GATK germline CNV can be used as an absolute copy number when multiplied by 2.
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Thank you so much.
May I know how I can make contig ploidy priors table needed to run DetermineGermlineContigPloidy?
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Hi Genevieve Brandt (she/her), Thank you for guidance above. I got denoised copy ratio after PostprocessGCNVCaller. Here, I have 2 queries. Please guide.
1. How I may get denoised ratio of all my samples in one file?
2. How to interpret absolute copy numbers? I calculated these by multiplying denoised copy ratio with 2. Most of my results are 4. As human genome ploidy is 2 so all those are duplicated?
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Hi Muhammad Shoaib Akhtar, for abnormal results, please make a new post with many details so we can look into it and determine what might be the issue.
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