Runs of homozygosity
--homozyg ['zs'] ['subtract-1-from-lengths'] ['cols='<column set descriptor>]
['pheno='<pheno name>]
--homozyg-maf <min nonmaj AF>
(alias: --homozyg-min-af)
--homozyg-snp <min SNP count>
--homozyg-kb <min length>
--homozyg-density <max inverse density (kb/SNP)>
--homozyg-gap <max internal gap kb length>
--homozyg-het <max hets>
--homozyg-window-snp <scanning window size>
--homozyg-window-het <max hets in scanning window hit>
--homozyg-window-missing <max missing calls in scanning window hit>
--homozyg-window-threshold <min scanning window hit rate>
--homozyg causes a set of run-of-homozygosity reports to be generated using PLINK 1.07's scanning algorithm. See the original documentation for more details.
- This analysis is most informative on a LD-pruned variant set: linkage disequilibrium extends runs that are not evidence of autozygosity. Use e.g. --indep-pairwise first.
- Relatedly, rare variants are homozygous in nearly everyone and pad out runs the same way. The default --homozyg-... parameter values make sense for human data filtered to minimum MAF ~0.05. So, as a sanity check, --homozyg now errors out when a MAF<0.05 variant is still present and --homozyg-maf, which applies a MAF filter specific to --homozyg, was not specified. (But if you're intentionally including rarer variants in your analysis, it's fine to specify "--homozyg-maf 0".)
- For phenotype-stratified counts in the .hom.summary file, specify "pheno=<pheno name>" on a binary or categorical phenotype.
- By default, segment bp lengths are calculated as (<end bp position> - <start bp position> + 1). This is a minor change from PLINK 1.07, which does not add 1 at the end. For testing purposes, you can use the 'subtract-1-from-lengths' modifier to apply the old formula.
- By default, only runs of homozygosity containing at least 100 SNPs, and of total length ≥ 1000 kilobases, are noted. You can change these minimums with --homozyg-snp and --homozyg-kb, respectively.
- By default, a ROH must have at least one SNP per 50 kb on average; change this bound with --homozyg-density.
- By default, if two consecutive SNPs are more than 1000 kb apart, they cannot be in the same ROH; change this bound with --homozyg-gap.
- By default, a ROH can contain an unlimited number of heterozygous calls; you can impose a limit with --homozyg-het. (This flag was silently ignored by PLINK 1.07.)
- By default, the scanning window contains 50 SNPs; change this with --homozyg-window-snp.
- By default, a scanning window hit can contain at most 1 heterozygous call and 5 missing calls; change these limits with --homozyg-window-het and --homozyg-window-missing, respectively.
- By default, for a SNP to be eligible for inclusion in a ROH, the hit rate of all scanning windows containing the SNP must be at least 0.05; change this threshold with --homozyg-window-threshold.
- You may also want to try 'bcftools roh', which uses a HMM-based detection method. (We'll implement a basic port of that command if there is sufficient interest.)
Population stratification >>
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