Fig. 3

Variation in the sensitivity and specificity of nucleotide variant calls and genotypes as a product of the depth of the sequence. Several 2 × 100 nt runs of WGS of sample NA12878 were generated and the sensitivity (red diamonds) and specificity (blue squares) of variant calls (a) or genotypes (b) by GSNAP/GATK-VQSR were examined by comparison with a reference set (GeT-RM/NA12878.NIST-GIAB_v.2.18) at depth of coverage of 10X to 100X