Adam English

Database tool has been refactored and placed into a repository at https://github.com/ACEnglish/tdb. @zqfang - Please try from that repository and if the error still happens, open a ticket there.

Hello, I am unable to recreate this issue. When I put the following input through `truvari collapse -i file.vcf.gz -o out.vcf` using v4.2.2-dev ``` ##fileformat=VCFv4.2 ##contig= ##FILTER= ##INFO= ##INFO= ##INFO=...

sounds good. Just know that SURVIVOR being elastic with the fields doesn't necessarily mean it is handling them properly. It doesn't have the most stringent VCF handling. It may be...

The logic for determining size is based on the vcf format specifications and documented [here](https://truvari.readthedocs.io/en/latest/truvari.html#entry-size). My first guess would be that your comp VCF is missing INFO/SVLEN and INFO/END, which...

Hello, Before I dig into this, could you confirm this behavior is present in Truvari v4.3.1? There were recent changes to the within/outside boundaries logic that may change what you're...

Please reopen if there's any updates.

Hello, The region we have documented for HTT from our Patho.csv is at chr4 | 3074876 | 3074966 | HTT | CAG -- | -- | -- | -- |...

Hey, Can you check which version of truvari you're using? I just tested and found that it was working. ``` % bcftools query -f "[%GT ]\n" test.vcf.gz ./. ./. ./....

This was in the 1kgp ONT data. Fritz has the snf files locally. https://www.biorxiv.org/content/10.1101/2024.04.18.590093v1.full.pdf