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6 weeks 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 • 166 views
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Entering edit mode
6 weeks ago
GokalpC ▴ 80
❯ plink1.9 --homozyg --help
(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.