D: 23 Sep 2023

Main functions

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Linkage disequilibrium

All of the following calculations only consider founders. If your dataset has a shortage of them, PLINK 1.9 --make-founders may come in handy.

Since two-variant r² only makes sense for biallelic variants, these collapse multiallelic variants down to most common allele vs. the rest.

Variant pruning

--indep-pairwise <window size>['kb'] [step size (variant ct)]
                 <unphased-hardcall-r^2 threshold>
--indep-pairphase <window size>['kb'] [step size (variant ct)]
                  <phased-hardcall-r^2 threshold>

--indep <window size>['kb'] [step size (variant ct)] <VIF threshold>

--indep-order <mode>

These commands produce a pruned subset of variants that are in approximate linkage equilibrium with each other, writing the IDs to plink2.prune.in (and the IDs of all excluded variants to plink2.prune.out). These files are valid input for --extract/--exclude in a future PLINK run; and, for backward compatibility, they do not affect the set of variants in the current run.

Since the only output of these commands is a pair of variant-ID lists, they now error out when variant IDs are not unique.

--indep-pairwise is the simplest approach, which only considers correlations between unphased-hardcall allele counts. It takes three parameters: a required window size in variant count or kilobase (if the 'kb' modifier is present) units, an optional variant count to shift the window at the end of each step (default 1, and now required to be 1 when a kilobase window is used), and a required r² threshold. At each step, pairs of variants in the current window with squared correlation greater than the threshold are noted, and variants are greedily pruned from the window until no such pairs remain.

--indep-pairphase is similar, except that it requires all genotypes to be phased (this is a change from PLINK 1.9), and looks at haplotype correlations.

Additional notes:

• --indep-order controls the order in which variant pairs are checked within each window.
• '1': Imitate PLINK 1.x.
• '2': Scan backwards within each window (default since 16 May 2023). This is usually faster.
• This operation can be slow, particularly when "--indep-order 1" is specified. You'll usually want to perform e.g. MAF-based filtering beforehand.
• On human data, some reasonable parameter settings are, in order of increasing strictness:
      "--indep-pairwise 100kb 0.8"
      "--indep-pairwise 200kb 0.5"
      "--indep-pairwise 500kb 0.2"

--indep-preferred <filename>

By default, when given a choice, the variant-pruning commands preferentially keep variants with higher nonmajor allele frequencies. However, if you provide a list of variant IDs to --indep-preferred, all variants in that list are prioritized over all variants outside it. (Allele frequencies will still be used for tiebreaking.)

LD statistic reports

--ld <variant ID> <variant ID> ['dosage'] ['hwe-midp']

To inspect the relation between a single pair of variants in more detail, you can use the --ld flag, which displays observed and expected (based on MAFs) frequencies of each haplotype, as well as haplotype-based r² and D'.

• By default, only hardcalls are considered in this computation; add the 'dosage' modifier to change this.
• When unphased calls are present, and there are multiple biologically possible solutions to the haplotype frequency cubic equation, all are displayed (instead of just the maximum likelihood solution identified by --r/--r2), along with HWE exact test statistics.

--bad-ld

PLINK 2 cannot estimate LD effectively when very few founders are present, so it normally errors out when there are less than 50. If you can't solve the problem with PLINK 1.9 --make-founders, you can use --bad-ld as a last resort to force PLINK 2 to proceed.

Sample-distance and similarity matrices >>