ROH ( Runs of Homozygosity Analysis)

Question

[always_learning]

Dear All,

I want to know about ROH analysis ? How to perform it ? How to interpret out put ROH resut data from tools like plink and bcftols roh etc etc. Is their any tutorial or papers available to learn understand and learn these concepts ?

Thanks Najeeb

Answer 1

[nsmi8446]

At what stage of the analysis are you at?

You can use BCFtools/ROH if you have a .vcf file. If you would like to use plink you will have to convert a .vcf file to the appropriate format.

If you use plink this section of the plink manual will help:

http://zzz.bwh.harvard.edu/plink/ibdibs.shtml#homo

If you use BCFtools/ROH this site will help:

https://samtools.github.io/bcftools/howtos/roh-calling.html

The introduction and abstract of these papers will potentially be useful:

https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btu401

https://academic.oup.com/bioinformatics/article/32/11/1749/1742869/BCFtools-RoH-a-hidden-Markov-model-approach-for

Answer 2

[always_learning]

Hi I know about all these tools. I am moreover asking about how you will interpret results from these tools ? Is their any tutorials somewhere which can help me to understanding this ?

Thanks