How to begin to use PLINK 2.0?

[Miwa Shinohara]

Hello. I am the beginner to use PLINK 2.0. Would someone please tell me how to begin to use PLINK 2.0?

[Christopher Chang]

If you're unfamiliar with PLINK, it's reasonable to start with the PLINK 1 tutorial at https://www.cog-genomics.org/plink/1.9/resources#teach .  Once you've worked through that, the PLINK 2.0 documentation should make more sense.

[Matthew Maher]

If you're really starting from nothing and want the friendliest (i.e. the least terse) introduction then I might suggest the highly readable PDF version of that PLINK 1 documentation:

http://zzz.bwh.harvard.edu/plink/dist/plink-doc-1.07.pdf  starting from chapter 2

I think it's useful to understand what is in a PED file, since it's informationally equivalent to a BED file, I believe. 

And I think it's useful to see the historical origins of PLINK1, as it may give you a better grasp of how PLINK 1.9/2 have built upon that legacy.

But Christopher will please correct me if I'm giving bad advice!

--
You received this message because you are subscribed to the Google Groups "plink2-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plink2-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/plink2-users/48499295-1a88-42bb-a661-3bbdac2bea06n%40googlegroups.com.

[Ashish Jayamohan]

I'm not an expert by any means, but I would suggest just doing some basic stuff that you know how to do from PLINK 1.9 or by yourself (allele frequency is my starting point). Read through the docs and figure out how you can expand from what you know into other sectors of the content. Also, I've found that I learn the fastest by just trying out new things (regardless of whether I have known it or not) on dummy data sets. Hope this helped!

Best,

Ashish J.