What Is The Best Tool To Detect Ibd In A Trio (Mom, Dad, Child)

Question

[Biomed]

I have snp data obtained from nuclear families and I want to detect "extended regions of autozygosity" using a tool. My current approach is to visualize SNPs in Genome Studio but I want to use a tool and automate this as a first pass scan before I do a manual inspection. Can tools like PLINK or Merlin be used successfully for this purpose, or do you have other suggestions?

Thanks

Answer 1

[Charles Warden]

I know that plink can be used to define IBD. Actually, plink1 and plink2 have different calculations - what you want in plink2 is called "KING"

I've typically used more samples, but I think it should be able to confirm the genome-wide relatedness for just a trio.

For example, you can see a measure of those king distance measures in the image towards the bottom of this post.

Answer 2

[Chaim]

You can try http://www.homozygositymapper.org/