Runs of homozygosity in Plink
Entering edit mode
2.7 years ago
Rafael • 0

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!

ROH Plink flags • 1.6k views
Entering edit mode
2.7 years ago
GokalpC ▴ 100
❯ plink1.9 --homozyg --help 
PLINK v1.90b6.22 64-bit (3 Nov 2020) 
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
--help present, ignoring other flags.

--homozyg [{group | group-verbose}] ['consensus-match'] ['extend']
--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
  * 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.


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


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.


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