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. 2011 Sep 28;12(9):R94. doi: 10.1186/gb-2011-12-9-r94

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Copyright ©2011 Sulonen 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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Correlation of sequenced genotypes to the SNP chip genotypes. SAMtools' pileup genotype calls recalled with quality ratios in the VCP were compared with the Illumina Human660W-Quad v1 SNP chip genotypes. (a) The correlations for Agilent SureSelect- and NimbleGen SeqCap-captured sequenced genotypes. (b) The correlations for SureSelect 50 Mb- and SeqCap v2.0-captured sequenced genotypes. Correlations for heterozygous, reference homozygous and variant homozygous SNPs (according to the chip genotype call) are presented on separate lines, though the lines for homozygous variants, laying near 100% correlation, cannot be visualized. The x-axis represents the accumulative minimum coverage of the sequenced SNPs.