Runs of homozygosity in Plink

Question

[Rafael]

I need to do my ROH search, and I don't know how can I put the flag of minimum SNPs per window. Anyone knows what is this flag, please? Thank you so much!

Answer 1

[GokalpC]

❯ plink1.9 --homozyg --help 
PLINK v1.90b6.22 64-bit (3 Nov 2020)           www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
--help present, ignoring other flags.

--homozyg [{group | group-verbose}] ['consensus-match'] ['extend']
          ['subtract-1-from-lengths']
--homozyg-snp <min var count>
--homozyg-kb <min length>
--homozyg-density <max inverse density (kb/var)>
--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>
  These commands request a set of run-of-homozygosity reports, and allow you
  to customize how they are generated.
  * If you're satisfied with all the default settings described below, just
    use --homozyg with no modifiers.  Otherwise, --homozyg lets you change a
    few binary settings:
    * 'group[-verbose]' adds a report on pools of overlapping runs of
      homozygosity.  (Automatically set when --homozyg-match is present.)
    * With 'group[-verbose]', 'consensus-match' causes pairwise segmental
      matches to be called based on the variants in the pool's consensus
      segment, rather than the variants in the pairwise intersection.
    * Due to how the scanning window algorithm works, it is possible for a
      reported ROH to be adjacent to a few homozygous variants.  The 'extend'
      modifier causes them to be included in the reported ROH if that
      wouldn't cause a violation of the --homozyg-density bound.
    * By default, segment bp lengths are calculated as <end bp position> -
      <start bp position> + 1.  Therefore, reports normally differ slightly
      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 variants,
    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 variant per 50 kb on average;
    change this bound with --homozyg-density.
  * By default, if two consecutive variants 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.
  * By default, the scanning window contains 50 variants; 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 variant to be eligible for inclusion in a ROH, the hit
    rate of all scanning windows containing the variant must be at least
    0.05; change this threshold with --homozyg-window-threshold.

--homozyg-match <> : Set minimum concordance across jointly homozygous
                     variants for a pairwise allelic match to be declared.
--pool-size <ct>   : Set minimum size of pools in "--homozyg group" report.

This is the help text from plink1.9 you may need to pay attention to your version. 1.07 or 1.9 or 2.0 may behave totally different.

--homozyg-window-snp

this flag is the scaning window size for the Sliding Window Algorithm.

--homozyg-snp

This is the flag for setting the minimum number of SNPs required to report a ROH.

Also may I urge you to try (shameless plug here :) )

ROHMM: Flexible HMM tool for Homozygosity detection

Don't worry about the pre-pre-alpha wording at the release. Just pull the latest master and build using the script provided. Needs Java only.