I'm trying to run some ROHs with Plink from a vcf file produced by GATK, with
GenotypeGVCFs. I set
BP_RESOLUTION and with
GenotypeGVCFs I included
When I run homozyg from Plink, I get 0 ROHs:
Options in effect: --allow-extra-chr --bfile out_name --homozyg Hostname: trueno128.hpc.csic.es Working directory: /home/ibe/gmochales/leopards/definitive/gvcf/ROHS Start time: Tue Mar 2 11:45:39 2021 Random number seed: 1614681939 32168 MB RAM detected; reserving 16084 MB for main workspace. 9911762 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. Total genotyping rate is 0.912456. 9911762 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 .
--included-non-variant-sites not working with the current version?
Thanks in advance!