Initial laboratory quality assurance relied on the GenCall score, a quality metric indicating the reliability of called genotypes that is generated by the BeadStudio software.
The quality value percentage is a quality metric that indicates the reliability of called genotypes generated by the SDS software.
The need for additional replication may also have been reduced by using elevated amounts of genomic DNA and the use of end-labeling rather than BioPrime may have increased the reliability of calls.
The same gold standard dataset was used by Major et al. (2013), who also examined the reliability of calling HLA alleles using NGS, but using the 1000 Genomes alignment data, and showed that this publicly available dataset can be used for this purpose, after appropriate filters (e.g., coverage) are applied.
Accompanying an increase in the reliability of each call, however, is a reduction in the overall call rate.
Each call is assigned a "SomaticScore", which indicates the reliability of the call.
The major improvements of the current draft, when compared with the previous version, are reflected in the number of annotated genes and, importantly, in the reliability of base call along the genomic sequence, as deduced from the very low number of internal SNVs.
We outline an empirical optimization approach to genotype calling in individual exomes, assess the reliability of genotype calling, and provide an overall evaluation of array-based exome capture followed by NGS analysis on the 454 platform.
The barrier called lack of clarity, relevance and reliability of research calls for change in researchers' objectives and methods, but we need to know what policymakers define as clear, relevant and reliable research, and why and when policymakers will use such research.
Furthermore, since each laboratory or company may have its own mutation calling algorithm, this lack of clarity means there is no consensus on how to ensure the reliability of mutation calls.
