How to Calculate Recall and Precision

[XuYan000131]

I have been following the workflow provided on your GitHub repository (https://github.com/friend1ws/nanomonsv/wiki/Tutorial) and using the COLO829 data provided to call somatic SVs. However, when comparing the results obtained from your software with the gold standard you provided (https://github.com/friend1ws/nanomonsv/blob/master/misc/example/v0.4.0/COLO829.nanomonsv.result.vcf) using the software (https://github.com/ACEnglish/truvari) to calculate recall and precision, I noticed discrepancies compared to the results reported in your paper. I suspect that these differences may be due to variations in the methods used to calculate recall and precision.

I am reaching out to you on GitHub to inquire about the specific methodology and algorithms you employed in your study to calculate recall and precision. I am particularly interested in understanding any specific considerations or modifications that need to be made in order to obtain comparable results. If you utilized any specific software tools or developed your own program for this purpose, I would greatly appreciate any insights or guidance you can provide.