Question: Detect the Runs of Homozygosity with the WGS data
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gravatar for zhang248
11 months ago by
zhang24830
HZAU, China
zhang24830 wrote:

Hi,

I'm using whole genome sequencing data to detect the ROH. I want to know which tool should I use, Plink or bcftools.

Thanks!

roh wgs • 424 views
ADD COMMENTlink modified 11 months ago by Kevin Blighe39k • written 11 months ago by zhang24830
3
gravatar for Kevin Blighe
11 months ago by
Kevin Blighe39k
Republic of Ireland
Kevin Blighe39k wrote:

If you already have VCF or BCF, then BCFtools may be better, and it even has a publication specifically for its ROH capabilities:

If you use PLINK, then you will have to first convert your data to PLINK format.

That said, PLINK has a more broad set of functions for filtering and QC of genetics data, so, would be a good choice.

My ultimate recommendation for you is to try both.

Kevin

PS - take a look here at these, too:

ADD COMMENTlink written 11 months ago by Kevin Blighe39k

Thanks Kevin, I have tried the Plink, I have tried Plink, but it seems that bcftools is better for detect the ROHs of whole genome sequence data according to the Bcftools/ROH paper and a review https://www.nature.com/articles/nrg.2017.109.pdf. How do you think about this?

ADD REPLYlink modified 11 months ago • written 11 months ago by zhang24830

Hello, also from my experience, BCFtools gave results that appeared to suit my hypothesis (and the hypothesis of my colleagues) on the data that we were analysing.

ROH analysis is not a primary aim of PLINK, of course, and PLINK has its own niche in association studies and family analyses. Undoubtedly, PLINK is one of the greatest programs of all time.

^ the diplomatic answer

ADD REPLYlink written 11 months ago by Kevin Blighe39k

Thank you, I'll try the BCFtools.

ADD REPLYlink written 11 months ago by zhang24830
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