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DeepVariant Accuracy Improvements for Genetic Datatypes

Thursday, April 19, 2018

Posted by Pi-Chuan Chang, Software Engineer and Lizzie Dorfman, Technical Program Manager, Google Brain Teamreleased DeepVariantgreater accuracy than previous methodsDeepVariant v0.6whole exome sequencingpolymerase chain reactionMany Types of Sequencing DataTruth Sets for Variant CallingDeep learningGenome in a BottleNational Institute of Standards and Technologyfirst benchmarking genome released by GIABInternational HapMap ProjectImproved Exome Model in v0.5v0.5 releasecodes for proteinsDNAnexustraining dataindelsingle nucleotide polymorphism

The total number of exome errors for HG002 across DeepVariant versions, broken down by indel errors (left) and SNP errors (right). Errors are either false positive (FP), colored yellow, or false negative (FN), colored blue. The largest accuracy jump is between v0.4 and v0.5, largely attributable to a reduction in indel FPs.

Improved Whole Genome Sequencing Model for PCR+ data in v0.6v0.6polymerase chain reaction

DeepVariant v0.6 shows major accuracy improvements for PCR+ data, largely attributable to a reduction in indel errors. Here we re-analyze two PCR+ samples that were used in external evaluations, including DNAnexus on the left (see details in figure 10) and bcbio on the right, showing how indel accuracy improves with each DeepVariant version.