Multiple samples in PLINK

Question

[Begonia_pavonina]

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?

Answer 1

[chrchang523]

You need to first use another tool to convert the GVCF to a regular VCF with more variants.

[Begonia_pavonina]

Thank you chrchang523. I didn't know we had to make a conversion of the gVCF file.

I have found gvcftools --merge_variants for this.

Is this the tools you were using?

https://sites.google.com/site/gvcftools/home/configuration-and-analysis