Han Cao

Hi @ekg and @glennhickey, I just found vcfwave may also output incorrect genotypes for biallelic input. In the below example, all SNPs' genotypes are missing. But they are not overlapped...

Hi @AndreaGuarracino , Just tried the latest `vcfwave` and it works well for the tested multi-allelic records. But it still incorrectly output missing genotypes for some SNPs that are not...

Sure, please find the vcf at [test.vcf.gz.txt](https://github.com/user-attachments/files/16421231/test.vcf.gz.txt). Below is the error message I got when using vcfbub: ``` > vcfbub -i test.vcf.gz thread 'main' panicked at 'called `Result::unwrap()` on an...

Hi, I am wondering if it is possible to use `vg snarls -A cactus` (or any other way) to deconstruct consistent variants between haplotype sampled graphs and the original graph?...

Hi @glennhickey , Thanks for the suggestion, I have tried calling variants on the full graph. I ran `vg deconstruct -a` and `vg call -A -a -z` with the same...