Calculate inbreeding coefficient out of ROH (Plink)

Question

[Manuela]

Hi everyone,

So I calculated the ROH with Plink and I was wondering how can I calculate from there the Inbreeding coefficient? Here is the code I used

plink --vcf SNP.final.vcf --keep-allele-order --allow-extra-chr --const-fid --homozyg --homozyg-window-snp 200 --homozyg-window-het 3 --homozyg-window-missing 5 --homozyg-window-threshold 0.05 --homozyg-snp 100 --homozyg-het 3 --homozyg-density 50 --homozyg-kb 100 --homozyg-gap 1000 --out ROH 

Thanks a lot!

[dr.fakharunnisa]

Hello Hope you find the solution for it till now. Can you please share? Is it the right way to add --het within the command for ROH)--homozyg)? I intend to find the FROH with the different kb distances. What to do for that?

The below paragraph is for explanation and it is from published paper to whom i am following:

PLINK v1.07 was used to estimate the genomic inbreeding coefcients based on ROH, popularly known as FROH and FROH for each animal is calculated as follows (McQuillan et al. 2008). In the present study, the mean of FROH was calculated as FROH>100 Kb, FROH>500 Kb, FROH>1 Mb, FROH>2 Mb, FROH>8 Mb, and FROH>16 Mb based on six ROH length classes.

Answer 1

[Dave Carlson]

You can get an estimate of the inbreeding coefficient (F) by adding the --het flag. See documentation here for details and caveats.

[Manuela]

Great, thanks a lot!