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mkirsche / Jasmine

Jasmine: SV Merging Across Samples
MIT License
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VCF (caller) concordance analysis using jasmine #30

Closed am8265 closed 2 years ago

am8265 commented 2 years ago

Hello,

Would you recommend this tool for SV VCF caller concordance analysis on Truth Set ? I have actually used this with max_dist_linear=0.1 min_dist=50 parameters, and used the SUPP_VEC field of the output vcf. Could this be a good approach beside other tools like this https://github.com/spiralgenetics/truvari ?

Thanks !

mkirsche commented 2 years ago

Hi,

Yes, that absolutely sounds like a good application for Jasmine! In our work we have used it to measure SV agreement to compare to ground truth, as well as to measure concordance across technologies and callers, and it has been useful for benchmarking in all of those settings. One note if you're comparing across callers is that you may need to use the --ignore_strand command line flag, particularly if comparing between Sniffles and other SV callers.

Feel free to reach out here if you have any further questions or encounter any issues using Jasmine for your concordance analysis!

Melanie