Shuo Cao

Hello, This VCF was produced by PGGB, which uses assemblies to construct the graph genome. Therefore there is only one genotype per sample. Or can we think of it as...

Thank you for getting back to me so quickly! There is one issue that may require further clarification. The mutation information for each sample is obtained from the assembly. However,...

Yes! That's it! But unfortunately, not all individuals were haplotype-resolved. so we get some samples named Ved and Ves, these samples are just primary assemblies.

Kindly suggest that trying to be compatible with the VCFs generated by [PGGB](https://pggb.readthedocs.io/en/latest/rst/quick_start.html#quick-start-example) or [Minigraph-Cactus](https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md) could be important. We usually use the set of variants they produce for downstream analyses...

Hi, I replaced the 1 in the VCF with 1/1; 0 with 0/0; and '.' with './.'. I tried treating all loci as homozygous, but it still resulted in this...

Thank you for the timely update. Regarding the mutation information, does ignoring Ns mean disregarding it entirely? This may not be appropriate in the current situation. Ignoring the whole variant...

Thank you so much ! I will test both options.

Hi I split the VCF file by chromosome. All chromosomes were successfully indexed except for chromosome 14, which reported the following error message: ''' (find_signatures_for_chunk_wrapper pid=82840) INFO:root:0/3 signatures removed because...

Hi ! My VCF contains only structural variations, about 280,000 of them, across 27 samples, at 1.8G. Thanks

Hi It works! Thanks a lot ! Best > On Jan 10, 2024, at 22:31, ivargr ***@***.***> wrote: > > > I've looked into this now, and think there might...