Deepvariant Structural Variants for ONT

google / deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

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Deepvariant Structural Variants for ONT #874

Closed DineshRavindraRaju closed 2 months ago

DineshRavindraRaju commented 3 months ago

Hi All,

When using the DeepVariant model type ONT_R104, does it also call structural variants (SVs), specifically ones between 0 and 30bp in length? We observe tools such as Sniffles and CuteSV typically identify SVs with a minimum length of 30bp, while Clair3 can detect SVs up to 50bp.

Thank you!

kishwarshafin commented 3 months ago

@DineshRavindraRaju, DeepVariant is a small variant caller and we do not train our models against the SV truth set. Generally SVs are defined to be variants that are 50bp+, so DeepVariant will not identify those. However, the INDEL length limit for DeepVariant is 50bp, so you can potentially see some variants called upto that range.