Question: What Is The Best Tool To Detect Ibd In A Trio (Mom, Dad, Child)
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gravatar for Biomed
8.3 years ago by
Biomed4.6k
Bethesda, MD, USA
Biomed4.6k wrote:

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

snp • 1.8k views
ADD COMMENTlink modified 6 weeks ago by Charles Warden7.5k • written 8.3 years ago by Biomed4.6k
2
gravatar for Charles Warden
6 weeks ago by
Charles Warden7.5k
Duarte, CA
Charles Warden7.5k wrote:

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.

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Charles Warden7.5k
0
gravatar for Chaim
8.3 years ago by
Chaim0
Chaim0 wrote:

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

ADD COMMENTlink written 8.3 years ago by Chaim0
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