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Hi @bhandsaker ,
I run 220 samples, 1 chromosome through the CNV discovery pipeline on recommended settings which generates this vcf gs_cnv.genotypes.vcf.gz, comprising of the metrics for each genotype and sample. I guess that I just pass this vcf in to the svgenotyper command, as for the deletion pipeline,. However, this outputs a similar file, i.e. without distinct genotype calls, 0/0, 0/1 etc. Am I doing something wrong? I didn't notice a CNV calling example in the test scripts.