Advice on conversion of multiple pairwise MAFs to multi-MAF

[microfuge]

Hi,

First of all, thanks for this amazing tool. Not only, it is fast but is structured so well that it is a joy to use.

This is from your comment in anchorwave repo. I have multiple pairwise MAF files (generated by anchorwave) for a common reference and multiple query genomes. I was wondering about the way to convert this into a multi genome MAF, based on the common reference genome.

This would be of great help to me as I can then use wgatools to call a multi sample VCF.

Thanks Again!

[wjwei-handsome]

Hi @microfuge ,

thanks for your use!

About converting multiple individual MAF alignments into ONE MAF, pafpseudo subcommand could generate pesudo-maf file from multiple query alignment PAF files based on a reference. But the reason it's called pesudo-maf is that this step ignores the insertion information.

For this part of the analysis, you can refer this repo: https://github.com/marbl/Primates?tab=readme-ov-file#code-availability and this BioRxiv: https://www.biorxiv.org/content/10.1101/2024.07.31.605654v1. The practice pipeline maybe you can refer is https://github.com/T2T-apes/ape_pangenome

About multi-sample vcf, I actually did consider the possibility of providing gvcf result for individuals to provide multi-sample joint-calling. But this is just an idea in my brain, it doesn't produce any line of code yet, oops 🙃

If you have any idea about this, please let me know :)

Hope this information can be helpful to you!

Best regards,
Wenjie