FilterForLinkage

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Objective

This protocol describes filtering SNP data for segregation distortion prior to linkage mapping.

The starting point for this protocol is our standard tab-delimited SNP format, where rows are loci, columns 1 and 2 are reference and locus respectively, and remaining columns are samples. You should first filter the SNP data as described in the [tutorial] to obtain a set of high-quality SNPs with relatively few missing data.

The following steps are basically only appropriate or required for linkage mapping; in other contexts these filters might remove biologically interesting signals.

For linkage mapping, we've found these filters are pretty effective at removing problematic samples and loci.

Step by step instructions

  • Filter for bad samples
  • Filter for bad loci

History

Created 23:00 Apr 03, 2017 By: EliMeyer

Last updated 09:02 Sep 23, 2019 By: EliMeyer