stschiff
commented
3 years ago You need phased data if you want to analyse multiple genomes. I can't support how to phase... that needs to be decided on a case by case basis. In humans, we typically use reference panels to do that, or related individuals.
You can also run MSMC2 on a single unphased diploid genome. Then it's pretty similar to PSMC. See also here for help:
https://link.springer.com/protocol/10.1007%2F978-1-0716-0199-0_7
Good morning, I am trying to use msmc2 with a non model species for which we do not have a reference panel for phasing, only population data. But the tutorial/example only shows the scenario when phasing with a reference panel and merging the individuals after. Would it be possible to have an example using msmc2 without the use of a reference panel? Because I'm a bit lost about how to proceed. Thanks a lot Best regards