DongLi

OK

> The issue is that `vg autoindex` isn't finding phased variants in the VCF, which are required to form the haplotype-specific transcripts in the pantranscriptome. Is your VCF un-phased? Hello!...

Hello! I would like to ask how to "phasing in your VCF", do you mean that this vcf needs to use bcftools for quality control?

[example.vcf.zip](https://github.com/jonassibbesen/rpvg/files/10915466/example.vcf.zip) I'm sorry to bother you again! I have read the recommended document according to what you said, but I am not very clear about how to carry out the...

Thank for your reply! First, l used the minigraph-cactus to establish a pan-genome which result in the primates-pg.vcf.gz primates-pg.gfa.gz. Secondly, l used the code "vg autoindex --workflow mpmap -t 20...

Ok, thank you for your reply. Wish you all the best! We will ask the developer about this, thanks.

> Hello, sorry for the delay. I phased my vcf using vcf_phase.py (https://ppp.readthedocs.io/en/latest/PPP_pages/Functions/vcf_phase.html). With this phased vcf the autoindex command is working now. Thank you for your help!

> > Thank for your reply! First, l used the minigraph-cactus to establish a pan-genome which result in the primates-pg.vcf.gz primates-pg.gfa.gz. Secondly, l used the code "vg autoindex --workflow mpmap...

Thanks for your feedback！ I'll then try the method you recommend for testing. Have a good day！

Thank you! I will test according to your suggestions and contact you if there are any questions. Have a good day!