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!
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zhang248 •
If you already have VCF or BCF, then BCFtools may be better, and it even has a publication specifically for its ROH capabilities: BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data
If you want to 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:
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?
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
Thank you, I'll try the BCFtools.
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