Large pedigree data

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dmans_sweet
Posts: 2
Joined: Thu Jan 19, 2017 9:47 am

Large pedigree data

Postby dmans_sweet » Thu Jan 19, 2017 10:08 am

I have a large sample of complex pedigrees (i.e. more than 100,000 subjects from 5 large "families") and want to calculate matrix of kindship coefficients for my data (this is not a GWAS data, only pedigree information). Software that I was using (solar) can't handle so many participants simultaneously to calculate the martrix.
Can I use GenAble for this? If not, could you recommend me another software or point me in the right direction? Any help will be appreciated, THANKS!

lckarssen
Site Admin
Site Admin
Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: Large pedigree data

Postby lckarssen » Thu Jan 19, 2017 5:17 pm

I don't think anybody ever used GenABEL with that many subjects. Maybe it works, maybe it won't.

Do I understand correctly that you don't have genetic data, only pedigree information? It has been a while since I used GenABEL for family data, but I seem to remember it only uses genetic data to determine the kinship matrix. As for other tools, I think that Plink2 also uses genetic data for kinship calculations.
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Lennart Karssen
PolyOmica
The Netherlands
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dmans_sweet
Posts: 2
Joined: Thu Jan 19, 2017 9:47 am

Re: Large pedigree data

Postby dmans_sweet » Fri Jan 20, 2017 1:01 am

Correct, only pedigree data is available.
I'm looking for software that can handle so many individuals at the same time to calculate kindship matrix.
Another possibility is to divide data to run analyses in batches of thousands of participants. Any ideas about any of that?

lckarssen
Site Admin
Site Admin
Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: Large pedigree data

Postby lckarssen » Fri Jan 20, 2017 8:54 am

Have you tried the kinship2 package? Not sure whether it has limitations in the nr. of samples.
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Lennart Karssen
PolyOmica
The Netherlands
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