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.
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