Handling of symbolic variants without ref sequence about truvari HOT 1 CLOSED

Hello,

Another user had a similar issue recently (#163). Truvari 4.1 (#164) has a change that will now warn users about using --pctsim != 0 and non-sequence-resolved calls (code). That post also has a script to help users fill in deletions, but I think you've already figured out that part. Needing to ignore sequence or altering the input VCFs isn't an ideal solution, but as callers (particularly those using long reads) are getting better at fully resolving SVs, and Truvari moves towards super accurate comparison (details) , and the VCF format specs are beginning to change the use of symbolic alts (details), the 'wild west' of SV representations seems to be shrinking.

Have a great day,
~/Adam English

from truvari.