--homozyg: Scan complete, found 0 ROH

[Kobiowu Abdulhadi]

Hi,

I am analysing ROHs from my data but kept getting "--homozyg: Scan complete, found 0 ROH" despite incoorperating all available solutions on the platform and other places. 

For my HaplotypeCaller step, I have used the following:

gatk HaplotypeCaller -R $reference -I $file1 -O $gvcf1 -ERC GVCF

gatk HaplotypeCaller -R $reference -I $file1 -O $gvcf1 -ERC BP_RESOLUTION 

For the GenotypeGVCFs:

gatk GenotypeGVCFs -R $reference -V $input.g.vcf.gz  -O $output_genotyped.vcf.gz

gatk GenotypeGVCFs -R $reference -V $input.g.vcf.gz --include-non-variant-sites true -O $output_genotyped.vcf.gz

I also selected SNP as my variants and hard filtered the snps. 

for the ROH step with plink:

plink --bfile medfly --homozyg-kb 500 --homozyg-window-snp 50 --out medfly_ROH --allow-extra-chr (I have used several variants of this line all returning the same results)

PLINK v1.90b6.21 64-bit (19 Oct 2020)          www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to medfly_ROH.log.
Options in effect:
  --allow-extra-chr
  --bfile medfly
  --homozyg-kb 500
  --homozyg-window-snp 50
  --out medfly_ROH

515835 MB RAM detected; reserving 257917 MB for main workspace.
3970776 variants loaded from .bim file.
1 person (0 males, 0 females, 1 ambiguous) loaded from .fam.
Ambiguous sex ID written to medfly_ROH.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 0.981855.
3970776 variants and 1 person pass filters and QC.
Note: No phenotypes present.
--homozyg: Scan complete, found 0 ROH.
Results saved to medfly_ROH.hom + medfly_ROH.hom.indiv + medfly_ROH.hom.summary

Your help would be highly appreciated.

[Christopher Chang]

This doesn't fully show how the "medfly" fileset was created, and it's likely that your mistake was in one of the steps you didn't show.

[Abdulhadi Kobiowu]

plink --vcf input.filtered.snp.vcf --make-bed -maf 0.05 --out medfly --allow-extra-chr --threads 24

That was how I created the medfly

************************

Abdulhadi Kobiowu,

Doctoral Researcher, Tu Lab,

Genetics, Bioinformatics and Computational Biology,

Fralin Life Sciences Institute,

Virginia Tech., US.

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[Christopher Chang]

The problem is with "--maf 0.05" here: think about what that does on a single-sample dataset.