Yumin Huang

> Please see here for documentation of the various formats > > https://github.com/vgteam/vg/wiki/File-Formats > > In particular, that page links to the Protobuf definitions for gam alignments > > https://github.com/vgteam/libvgio/blob/eb1fe76878aff8f26f0a2f38a1c133ec2f353e57/deps/vg.proto#L109-L151...

In my set of orthologous groups, no strict single-copy orthologs were identified; rather, each group contains multiple gene copies per species. I am considering randomly selecting one gene from each...

Thanks for your quick reply. So, if I want to use polyploid vcf as input, is there any way or process to make the index as accurate as possible and...

> You could try breaking polyploid samples into haploid samples. For example, if you have n haplotypes of sample `sample`, you can transform them into samples `sample_1` to `sample_n`. If...

> If your most / all of your variants are unphased, as you seem to imply, it's probably best to just drop the genotypes from the VCF completely. The haplotype...

Hi! @jltsiren I am not sure whether constructing separate GBWTs for the reference, haploid genotypes, and polyploid unphased genotypes separately (ref.gbwt, hap.gbwt, poly.gbwt) and subsequently merging them is appropriate for...