Figure 6.

Comparison of MiST and GATK. Each box has three sets of numbers, from left to right they are variant calls, (i) unique to MiST, (ii) common to both platforms and (iii) unique to GATK. Filters are applied to remove calls occurring in public databases like dbSNP (17), 1000 Genomes (18) and a collection of already known private variants. MiST called 14 808 variants from dbSNP and 1000 genomes as opposed to 7468 variants by GATK. MiST had more variants in common with the exonic genotyping array, compared with GATK. In the box shaded orange, of the 96 calls unique to GATK, 25 calls map to multiple locations, 35 calls were far from exonic boundaries, 6 calls were eliminated by MiST for arising in low complexity regions such as a run of T’s, 14 calls were eliminated by MiST due to clonality corrections. In addition, there were 16 calls private to GATK (7 in UTRs, and 9 synonymous calls) that were not called by MiST, because the exons are not present in RefSeq.