Stephan Schiffels

Hi @vlnaraujo. Yes, MSMC2 is in bioconda. I think with de novo assemblies you would still use alignment data, but you align all of your short-read data to the de-novo-assembled...

No idea. I'm afraid I can't support nohup, nor how to run bcftools. If it helps, you can split up the pipeline and first generate the pileup-output into a separate...

I have zero experience with this and don't even know what "HiFi" reads are, I'm afraid.

I have for now added a line to the README, and might pick this up in the future

Yes, in this case phasing is needed. I don't fully get your list of indices. You can certainly prepare your input file for three populations, but the estimation should focus...

Out of the top of my head, I see two problems: 1.) Some of your input data contain 0 SNPs. I think you should remove them from the input. 2.)...

Hmm, I'm not sure I understand the contexts of the two quotes above. I can't remember what's exactly in the book, but I guess the way to plot curves and...

Those are minor differences. Just look at the scripts and judge whether the calculation makes sense to you. It's just linear interpolations. Not sure what to advice here.

Well, your files have extremely different lengths. One has a few dozen sites, the other many more. You seem to be missing a hole bunch of sites from your 16-haplotype...

Well, but how can I possibly know what went wrong with the creation of your file?