A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree

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Figure 4.
Figure 4.

Precision versus recall in NA12878 evaluated against the Platinum catalog data set. Triangles, circles, and squares, respectively, represent the results from 30×, 40×, and 50× sequencing depth for Platypus (red), FreeBayes (blue), GATK3 (green), and Strelka (black). Excluding Strelka, all callers are run in joint calling mode incorporating the parents. (A) Indels (large symbols) and SNV (small symbols) results plotted on the same axis. (B) Expansion of SNV results, also showing ROC curves for GATK3 and Strelka that reflect the trade-off of recall versus precision that is obtained by altering specific variable parameters when using the algorithms.

This Article

  1. Published in Advance November 30, 2016, doi: 10.1101/gr.210500.116 Genome Res. 27: 157-164

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