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The T m was a temperature which corresponds to the peak value of a derivative melting curve plotted using the 'T m calling' method.
The genotype calls are likely sufficiently reliable since comparisons between r2 values generated from this SNP calling method and from the stricter SNP calling method described below under "Vitis9KSNP array" were highly correlated (r2 = 0.95, p<1×10−15).
Using our accurate variant calling method for pooled sequence data, we were able to not only identify single nucleotide variants with a low false discovery rate (<1%) but also accurately detect short insertion/deletion variants.
This dual threshold peak calling method was used to be more inclusive than 1% FDR (which identified very few peaks in a number of our datasets) and still limit the number of peaks called at 5% FDR.
The CLOZUK calling method is described in Guha et al. (2013) (52).
Thus the specificity of the arrays and calling method is 498/498+159: 78%.
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Several groups have developed SNP calling methods based on pooled sequencing data [ 7, 9- 12].
Therefore, CNV calling methods are strongly de-sired to control the FDR [ 7].
This will be called method HC henceforth.
Using Spearman's correlation is called method SP henceforth.
The four methods were called method N, B, C and T [[ 20, 46- 48], respectively].
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