Hi all,

I have recently tried to estimate runs of homozygosity (ROH) from my vcf file by using plink 1.9.

I ran following code to generate binary files that plink required:

    plink --vcf myfile.vcf --make-bed --out out_name --no-sex --no-parents --no-fid --no-pheno --allow-extra-chr

This vcf file only contains one individual and about 3 million SNPs.

I used --allow-extra-chr here because I mapped my sequences to a drift genome.

Then, I used following code (with default parameters), trying to estimate ROH of my sample:

    plink -bfile out_name --homozyg --allow-extra-chr

The result gave me 0 ROH, and only header produced in .hom file.

I also tried different parameters with different SNP windows and criterions, such like:

    plink -bfile out_name --homozyg --homozyg-window-snp 50 --homozyg-snp 50 --homozyg-window-missing 3 --homozyg-kb 100 --homozyg-density 1000 --allow-extra-chr





However, all the results were the same, that showed :

 


    PLINK v1.90b6.12 64-bit (28 Oct 2019)          www.cog-genomics.org/plink/1.9/
    (C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
    Logging to plink.log.
    Options in effect:
    
      --allow-extra-chr
      --bfile out_name
      --homozyg
      --homozyg-density 1000
      --homozyg-kb 100
      --homozyg-snp 50
      --homozyg-window-missing 3
      --homozyg-window-snp 50
    
    515905 MB RAM detected; reserving 257952 MB for main workspace.
    3708761 variants loaded from .bim file.
    1 person (0 males, 0 females, 1 ambiguous) loaded from .fam.
    Ambiguous sex ID written to plink.nosex .
    Using 1 thread (no multithreaded calculations invoked).
    Before main variant filters, 1 founder and 0 nonfounders present.
    Calculating allele frequencies... done.
    3708761 variants and 1 person pass filters and QC.
    Note: No phenotypes present.
    --homozyg: Scan complete, found 0 ROH.
    
    Results saved to plink.hom + plink.hom.indiv + plink.hom.summary .




Does anyone have idea why this happened to my files?

Will be grateful for any suggestions.

 
This is unsurprising if your VCF contains only positions where your sample *differs* from the reference genome; practically all the ROHs will span regions which are excluded by your VCF.  You may need to reconstruct your VCF in a way that includes homozygous-REF calls in an unbiased manner.