Joshua Penalba

Thanks Pasi! I get what the issue was. I was misunderstanding the whole half sib thing and kept including it into the full sib families. Now I get that ParentCall just looks for the half sibs in the other full sib families. In hindsight, I now understand what you've been trying to tell me about only having only full sib families organized. Seems quite trivial but I kept missing the point. Thanks for your patience!

Here's the pedigree file but I used a script to join this and the posterior file.

Dear Pasi, Thanks for that. I've organized the input file but have been getting an error. This is ddRAD data that I mapped onto a draft genome assembly using BWA. I then used your scripts to generate the posterior file. I split the pedigree into ~40 full sib families with at least 2 offspring. Where available, I included the grandparents, half sibs, with the alternate parent of the half sibs. If I have a parent missing but many offspring, I created DUMMY individuals with 1 1 1 1 1 1 1 1 1 1 posteriors....

Thanks for the rapid reponse, Pasi! So when running ParentCall2, I would include the half sibs, their alternate parent, and the grandparents of the original parents? Then for the other modules I would only use the full-sib families? I'm trying it out now. Best, Josh

Hi Pasi, I have a complex pedigree from a wild population of birds with a lot of extra pair paternity (lots of half-sibs some of which with genotyped fathers and some without). I have about 280 birds through 9 generations for ~26K SNPs. As I prepare the input file, I was wondering how to best organize the birds into families. Would I split them into many 2 or 3-generation families or lump them into fewer multi-generation families? I was previously using your older CRIGEN + CRIMAP combo to organize...

Hi Pasi, Thanks for the response. Glad to hear that Lep-MAP3 can handle half-sibs!...

PS. When I say complicated, I mean it looks like this. Where the dotted lines link...

Hi Rasi, I'm about to try LM2 for a fairly complex pedigree of a natural population...