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PapenfussLab / gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite
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GRIDDS results benchmarking queries: #649

Closed poddarharsh15 closed 11 months ago

poddarharsh15 commented 11 months ago

Hello, I'm attempting to benchmark GRIDSS output using Truvari with GIAB truth sets. However, I've observed that a significant portion of the structural variant (SV) detections are labeled as BND (breakend) rather than DEL (deletion), INS (insertion), or DUP (duplication). I'm seeking guidance on the possible methods to accurately identify and categorize these BND events into DEL, INS, or DUP. Your assistance is greatly appreciated. Thank you.

d-cameron commented 11 months ago

https://github.com/PapenfussLab/gridss?tab=readme-ov-file#why-are-all-calls-bnd

poddarharsh15 commented 10 months ago

Hello, Thank you for your previous response. I attempted to use simple-event-annotation.R but encountered errors. Despite this, I managed to generate the .vcf file with INS;DUP;DEL events. Could you please review the error details attached and provide any insights or suggestions for resolution? Screenshot from 2024-01-02 15-57-56