Hello everyone, I have tried to input a GVCF file in PLINK to detect Runs Of Homozygosity (ROH) using the following scripts:
plink --vcf GVCF_SNPs_edit.vcf --homozyg --out GVCF_SNPs --allow-extra-chr --no-parents --no-sex --no-pheno --homozyg-window-snp 50 --homozyg-snp 50 --homozyg-window-missing 3 --homozyg-kb 100 --homozyg-density 1000
Unfortunately, it seems that the GVCF file is not processed correctly.
There is far less ROH detected in this file than in the separated samples files concatenated.
I think PLINK detects the ROH in common for all the samples in the GVCF.
Has anyone tried it? If yes, do you know how to prevent it?