What are the major differences between plink and plink2?
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6.0 years ago
MAPK ★ 2.1k

Hi, I was running plink(1.9) tool to create bed file (plink --file inputfile --make-bed --noweb --out outputfile) which worked fine, but when I switched to plink2, the same command doesn't work. Can we do everything that plink(1.9) does with plink2? Can someone please clarify this? Thank you.

plink • 6.5k views
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I don't think plink2 does --noweb. It is probably assumed by default now.

EDIT: Looks like the differences are much more extensive. See https://www.cog-genomics.org/plink/2.0/input

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Even this command doesn't work: plink2 --file inputfile --make-bed --out outputfile

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I don't think --file is accepted

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I was creating .bed file using inputfile.ped and inputfile.map. I was able to do it with plink, but not with plink2. What could be the reason?

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I think you still need plink to get to the binary files! Odd!

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Not sure why - I've never used plink2 myself

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I mostly began using plink at version 1.9; so, have witnessed the shift-over to plink2. I believe, correct me if wrong, that the release of plink2 mostly coincided with the original authors 'moving on' in their respective careers (and the licensing to Cog Genomics). However, plink2 is still maintained by Christopher Chang, who is active on Biostars.

I think that plink2 is much comprehensive and there is a lot of ideas listed on the home-page in terms of future development work.

Unfortunately, a question like this can really only be answered by one of the developers.

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5.6 years ago

Sorry about not noticing this earlier.

The main difference is that plink 1.9 is essentially finished, while plink 2.0 is an alpha-stage program which will have significant unfinished components for a while to come. As a consequence, current development priorities for plink 2.0 are centered around things which are impossible to do with plink 1.9, such as handling multiallelic/phased variants and dosage data and reliably tracking REF/ALT alleles; while things that plink 1.9 already handles perfectly well, such as working with .ped/.map file pairs, have been deliberately deprioritized for now.

So, you should stick to 1.9 as long as it's good enough for the jobs you need to perform. But once you need to do something outside 1.9's scope, you're likely to find that 2.0 already has the additional feature you need (or it'll be added quickly after you ask for it).

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