Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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.