Hi everyone! I’m looking to validate germline CNV calls from WGS data using the

variantbenchmarking

pipeline (with calls generated via CNVKit), but I’m having trouble identifying a suitable truth set for comparison. Has anyone had experience with a reliable CNV truth set that they’d be willing to recommend or share? Any help or advice would be really appreciated! 🙏

Hello, as far as I know there are two sources: https://zenodo.org/records/14619054 for SEQC2 and https://zenodo.org/records/7515830 for COLO829

Thanks so much for the helpful links, @Kübra Narcı — I really appreciate you taking the time to share them! I’m actually hoping to benchmark germline CNVs specifically, so I was wondering if you'd be happy to share any germline CNV truth sets that you’d recommend using? Thanks so much again for the help!

sorry! I have missed that. As far as I know, there is no CNV published for germline. Maybe what you can do is to filter out DUP type from HG002 SV? https://www.nature.com/articles/s41587-020-0538-8

This is super helpful Kübra, thanks so much for sharing!