Plink Step by Step for non FBAT (family based association test)

• This section assumes that Plink Step By Step has already been completed.
• Rather then spend all of our time on family based studies I would like to give you all an idea of the differences between FBAT and normal association tests with
• Lets say you have data and you want to perform a normal association test on a binary or a continuous variable.
• By normal association test we mean we will not be performing a FBAT.
• As a quick review, lets look at our plink workflow again.

• Lets also take a look at the start of the fam file we were using again:

1130 5136-SB-0678 5136-SB-0680 5136-SB-0679 1 2
1130 5136-SB-0679 0 0 2 1
1130 5136-SB-0680 0 0 1 1
1225 5136-SB-0663 5136-SB-0665 5136-SB-0664 1 2
1225 5136-SB-0664 0 0 2 1
1225 5136-SB-0665 0 0 1 1

• What would the file look like for a binary variables and a non FBAT?

1130 5136-SB-0678 0 0 1 2
1130 5136-SB-0679 0 0 2 1
1130 5136-SB-0680 0 0 1 1
1225 5136-SB-0663 0 0 1 2
1225 5136-SB-0664 0 0 2 1
1225 5136-SB-0665 0 0 1 1

• Finally, what would the file look like for a continuous variable and non FBAT?

1130 5136-SB-0678 0 0 1 2
1130 5136-SB-0679 0 0 2 10
1130 5136-SB-0680 0 0 1 11
1225 5136-SB-0663 0 0 1 3
1225 5136-SB-0664 0 0 2 22
1225 5136-SB-0665 0 0 1 44

With just these differences in our FAM file the latter two can be tested using the following command, which is very similar to the TDT command we performed in the previous section.

• --assoc will work for continuous and binary data
• Other association tests: This link provides more info on other types of association tests which will get beyond the scope of what we can teach in this course.

call11="plink --bfile ${outpath}/cleanedME_${sample} --assoc --freq --adjust --out ${outpath}/tdt_${sample}"
echo $call11
eval $call11

Start Group Exercise 1: (30 mins)

• Take the flowchart figure above and within your group discuss what the main differences would be for a non FBAT. (for example as binary non FBAT or a continuous non FBAT)
• I suggest just copying and pasting into powerpoint as a group and marking up the workflow.

Side note:

• While we work on this exercise do you have any other types of analysis you are interested in? Think about how these might fit into such a workflow and see if Plink has options for them. We have covered a workflow and if you understand all of the components it should be fairly easy to update and customize to your interests. If we have time we can try to discuss some of these in a bit more detail.
• It still goes without saying that there are tons of other software out there for GWAS studies beyond plink, unfortunately we do not have time to cover them all.

End Group Exercise 1, Break

Discussing the answers to the above question. 5 minute break.

• FAM file would likely have a different format (see above examples)
• IBD check will have different expectations
• wAnnovar may not be relevant if working on non-human organism.
• if non FBAT then mendelian errors not necessary.
• –assoc may be used and PCA covariate adjustment may be needed for large popluation differences