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. 2015 Mar 7;16(1):155. doi: 10.1186/s12864-015-1310-1

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© Bassil et al.; licensee BioMed Central. 2015

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Six SNP quality classes (A) and four variance filters (B) applied to the PHR genotype class. A. Default SNP quality classes produced by the Axiom Best Practices Genotyping Workflow. B. An example cluster plot for a SNP identified with each of the four variance filters used including: AB.varY identified large heterozygous cluster variance in the Y dimension; AA.varY for homozygous (AA) variance in the Y dimension; BB.varY, for homozygous (BB) variance in the Y dimension; and AB.varX, for heterozygous variance in the X dimension.