  Clinical adoption of human genome sequencing requires methods with known
accuracy of genotype calls at millions or billions of positions across a
genome. Previous work showing discordance amongst sequencing methods and
algorithms has made clear the need for a highly accurate set of genotypes
across a whole genome that could be used as a benchmark. We present methods to
make highly confident SNP, indel, and homozygous reference genotype calls for
NA12878, the pilot genome for the Genome in a Bottle Consortium. We minimize
bias towards any method by integrating and arbitrating between 14 datasets from
5 sequencing technologies, 7 mappers, and 3 variant callers. Regions for which
no confident genotype call could be made are identified as uncertain, and
classified into different reasons for uncertainty. Our highly confident
genotype calls are publicly available on the Genome Comparison and Analytic
Testing (GCAT) website to enable real-time benchmarking of any method.
