CNV-calling single sample
Entering edit mode
4 weeks ago
Boberoni ▴ 10

Dear all,

I am working on a pipeline that should include Copy Number Variation calling (next to variant calling and some other stuff).

To test the pipeline I use the NA12878 dataset from the GIAB project.

For CNV-calling I tried using GATK 4 best practice (which uses DetermineGermlineContigPloidy and GermlineCNVCaller). It seems like this tool can be used for a single sample but you need a model to compare your called CNV with. (

I can't find clear documentation on how to construct such a model and considering I only have a single sample, I can't run it in cohort mode.

Does anyone know how to get such a pre-build model or how to construct it when you only have one sample?

Otherwise, any recommendations on CNV-calling tools that suit this approach better?

I am fairly new to CNV-calling so any answers or advice are helpful! :)

copynumbervariation cnv GATK na12878 • 126 views

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