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refMapper_matrix

Overview

refMapper_matrix generates a SNP matrix (not a distance matrix) file from GFF files. (Usually the GFF files will have been created as annotations of SNPs subsequent to alignment of assemblies' sequences versus a reference assembly by refMapper.)

The refMapper_matrix pipeline is usually invoked as part of a workflow to create a SNP tree.

refMapper_matrix is currently in version 2.0.

Summary

refMapper_matrix reads GFF files (generally expected in a specific format written by refMapper) that each annotate mutations in a genome assembly and also regions that successfully align with the reference, repetitive regions and regions with uncertain base calling or ambiguous alignment. It outputs a single SNP matrix file for all of the assemblies which documents mutations and their type (including identity, synonymous and non-synonymous SNPs, stops and frameshift mutations) at positions in the genome assemblies that have variation.