Question regarding somatic CNVs and Per-sample genotype filter

Max_IT

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Feb 21, 2025, 5:03:02 AMFeb 21

to delly-users

Hi,

Thank you for creating Delly and making it available to the community. I am working with cancer samples and using your pipeline to determine CNVs. I am trying to find a description for the "Per-sample genotype filter" FORMAT field in the CNV workflow, but Google did not help much. Can you please help?

I have found some description related to SVs here: https://github.com/dellytools/delly/issues/205 . I am not sure if applies to CNVs as well, and I would like your thoughts about using it as a parameter to filter off CNVs by itself, or in conjunction with other parameters.

Best,
Max

Tobias Rausch

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Feb 26, 2025, 7:41:52 AMFeb 26

to Max_IT, delly-users

Yes, it's similar for CNVs as for SVs. The FORMAT GQ value assesses how well the best copy-number (CN) state prediction is separated from the second best CN state prediction. If FORMAT GQ < 15, the FORMAT FT field is set to LowQual.

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Max_IT

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Feb 26, 2025, 9:43:23 AMFeb 26

to delly-users

Thank you for your kind answer and for clarifying the meaning of the field, I appreciate it.

Best,
Max

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