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. 2014 May 15;42(12):e101. doi: 10.1093/nar/gku392

Table 5.

Summary of Ti/Tv ratios of SNP call sets derived from new and old versions of GATK and different mappers

graphic file with name gku392tbl5.jpg

Summary of Ti/Tv ratios of SNP call sets derived from the new (V2.0 up to V2.2.4) or old (up to V1.6.7) versions of GATK and different mappers including Eland and BWA. *Name designation for variations of GATK versions and mappers in the following format:

GATK_version_NumSample(option)_MapperContigOptionsForBWA(Option)_Mapper_VQSRThreshold. Version: V1 or V2 of GATK; NumSample: optional, if 5S, 5 samples with trio relations; if 17S,17 samples in larger family; MapperContigOptionsForBWA: optional, if NC; no contigs in genome reference; C: with contigs in genome reference. Mapper: BWA or Eland methods.; VQSRThreshold: VQSR threshold as 099 for 0.99 or 090 for 0.90.