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. 2013 Mar 27;5(3):28. doi: 10.1186/gm432

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Copyright © 2013 O'Rawe et al.; licensee BioMed Central Ltd.

This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Mean indel concordance over 15 exomes between 3 indel-calling pipelines: GATK, SOAPindel, and SAMtools. Mean concordance was measured between (A) all indels, (B) known indels (indels found in dbSNP135), and (C) unknown indels (indels not found in dbSNP135). Indels were left normalized and intervalized to a range of 20 genomic coordinates (10 coordinates on each side of the normalized position) to allow for a reasonably standardized indel metric for comparison. To determine whether or not indels were matching, the genomic coordinates as well as the base length and composition of each indel were considered.