‘truvari collapse -k maxqual‘ does not work for me about truvari HOT 4 CLOSED

Thank you so much for reporting this. Indeed there was a problem with the ordering. I was returning a bool instead of int for my functools.cmp_to_key functions. Develop now has a fix if you'd like to test using that. This is a big enough problem that I'll try to cut an official v3.3 release soon

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Thank you for your quick reply! So no matter how the parameters are set, is the first row kept by default?
By the way, I noticed overlapped SVs in the same sample were reported occasionally by some SV detection software (for example, Manta). For cohort-level VCF, re-genotyped after merging all individuals may also introduce overlapping SVs in the same sample.
Have you ever had similar issues and do you have any recommendations for solutions?

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I believe with v3.2 the first variant was always kept regardless of --keep. However, the fix for this also exposed that there was a lack of enforced determinism in the sorting. So the safest assumption is that it was just randomly picking a variant. I also just put in dbdbe55 which will help collapse more consistently choose alleles.

I think it would take a long time to fully answer your question - it is a complex subject, to say the least. But, I can point you to our preprint where one of the things we try to show is that there is more allelic diversity than other SV merging tools report. The point being that I have observed overlapping SVs and believe in being cautious about over-merging.

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Interesting research! Thanks again for the useful tool！

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