Updated comparison of variant detection methods: Ensemble, FreeBayes and minimal BAM preparation pipelines

Variant evaluation overview I previously discussed our approach for evaluating variant detection methods using a highly confident set of reference calls provided by NIST's Genome in a Bottle consortium for the NA12878 human HapMap genome, In this post, I'll update those conclusions based on recent improvements in GATK and FreeBayes. The comparisons use bcbio-nextgen, an…