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. (https://gatk.broadinstitute.org/hc/en-us/articles/360042912371-DetermineGermlineContigPloidy#--model)
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! :)