1 SNP per fragment

[Antonio Varas Myrik]

Hi friends:

I want to retain only one SNP per fragment to avoid LD in a landscape genomic study. Some idea of how do it?

Thanks in advance

Antonio

[Arthur Georges]

Hi Antonio,

Use

gl <- gl.filter.secondaries(gl,verbose=3)

Filters loci that represent secondary SNPs in a genlight object

Description

SNP datasets generated by DArT include fragments with more than one SNP and record them separately with the same CloneID (=AlleleID). These multiple SNP loci within a fragment (secondaries) are likely to be linked, and so you may wish to remove secondaries.

This script filters out all but the first sequence tag with the same CloneID after ordering the genlight object on based on repeatability, avgPIC in that order (method='best') or at random (method='random').

The filter has not been implemented for tag presence/absence data.

Usage

gl.filter.secondaries(x, method = "random", verbose = NULL)

Arguments

x	Name of the genlight object containing the SNP data [required].
method	Method of selecting SNP locus to retain, 'best' or 'random' [default 'random'].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].

A

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