Calculating ROHs and Heterozygosity from GATK

Question

[gubrins]

Heys everybody,

I'm trying to run some ROHs with Plink from a vcf file produced by GATK, with HaplotypeCaller and GenotypeGVCFs. I set -ERC from Haplotypecaller as BP_RESOLUTION and with GenotypeGVCFs I included --included-non-variant-sites true.

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 .

Is --included-non-variant-sites not working with the current version?

Thanks in advance!