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

Table 3.

Summary of Mendelian inheritance error rates on SNPs derived from the new and old versions of GATK and different mappers

graphic file with name gku392tbl3.jpg

Summary of Mendelian inheritance error rates amongst the chosen family trio members (samples #9, #10 and #2; Supplementary Figure S1) for the SNPs detected with 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 thresholds as 099 for 0.99 or 090 for 0.90. Similar results were obtained for the other two trio sets (with sample #3 or #4 as child) available in the family (data not shown).