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. 2015 Sep 18;5:14283. doi: 10.1038/srep14283

Figure 4. Consistency evaluation using rare variants from 3 sequencing data sets for NA12878.

Figure 4

The 3 data sets were generated by 1000 Genomes project and AllSeq (HiSeq-D, HiSeq-J). We used the same alignment algorithms (BWA-MEM) as the primary focus is to compare variant callers. For each data set, 4 variant callers were used to call variants, variants with MAF > 1% were dropped. The remaining variants from 4 callers were merged in different ways to get consensus calls. For each variant calling method, we plotted a Venn Diagram comparing overlapping of variants among the 3 data sets (A,B). The percentages show the proportion of variants shared by 3 data sets.