Dear all,
I want to use MSMC2 and eSMC and want to follow the guide which can be found on the github page of MSMC (https://github.com/stschiff/msmc/blob/master/guide.md and https://github.com/stschiff/msmc-tools). The guide mentions that you need to create a mappability mask per chromosome using SNPable (http://lh3lh3.users.sourceforge.net/snpable.shtml) if you don't have one.
The website from SNPable was last modified in 2009 and it's states that it is an unfinished page - I thought that there might be a better alternative to do it.
Does someone know a newer/better method to do it?
I also think that the documentation of this tool is really sparse. Can someone explain to me what the steps of SNPable mean or where I can find more explanation?
Thanks in advance.
Hello, Laura! I have the same problem with creating mappability masks for MSMC2 with SNPable. Have you solved it?
Hello. Did you manage to run SNPable? I tried running MSMC2 without the mask files and it did work, I also create the plots. I don't know what the mappability maks does and if we need it. I'm a little lost.