I am using GATK3 on GCP for CNV analysis os WES and WGS data from Germline using default options. it does not give error but the number of variants I am getting is significantly less (less than half compare to the pipeline I have on local cluster). I am trying to do such analysis on the cloud not local cluster that is why I am using one of the workflows which already exits on GCP. do you know what the problem is that I do not get all the variants?
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