Additional file 9.

Correlation of SAMtools' pileup genotype calls (a, b) and GATK genotype calls (c, d) from Agilent SureSelect- and NimbleGen SeqCap-captured and SureSelect 50 Mb- and SeqCap v2.0-captured sequenced genotypes to the Illumina Human660W-Quad v1 SNP chip genotypes. The SAMtools' pileup genotype calls correlated worse with the chip genotypes than the genotypes accommodated with the quality ratios. Correlations for heterozygous, reference homozygous and variant homozygous SNPs (according to the chip genotype call) are presented in separate graphs, though graphs lying near 100% correlation cannot be visualized. The x-axis represents the accumulative coverage of the sequenced SNPs.

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Sulonen et al. Genome Biology 2011 12:R94   doi:10.1186/gb-2011-12-9-r94