Stephan Schiffels

Could it just be that you use `--trio 1,2,3 --trio 4,5,6` when it should actually be `--trio 0,1,2 --trio 3,4,5`? My indices are all 0-based, not 1-based.

Is the plant selfing? Could the extremely low population size be due to long blocks of homozygosity? That would then also screw up the cross coalescence rate

You have to split the input by chromosome.

I think you need to run every chromosome separately.

No, they're independent. The individual masks gives regions at which the individual has enough data. The mappability mask gives regions in the genome which are generally mappable. The code will...

Start with a few and then see whether you get different results if you run on more.

OK, this is complicated. MSMC determines the time-boundaries from the average heterozygosity of the input data. Of course, with different masks you may get different thetas, so time will be...

Ah OK. So incorrect phasing may have moved mutations in biased ways onto haplotypes, so that some haplotypes were much more similar than expected. Interesting, but not too surprising given...

OK, I haven't touched the tutorial for a long time, but you're right, I should revisit it and update all the necessary plots. It's not super high on my todo...

Hmm, not sure. Have you checked whether there is evidence for a recent contraction here? For example via runs of homozygosity? Otherwise I don't know. Have you compared these results...