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Background  Supervised learning from high-throughput sequencing data presents many challenges. For one, the curse of dimensionality often leads to overfitting as well as issues with scalability. This can bring about inaccurate models or those that require extensive compute time and resources. Additionally, variant calls may not be the optimal encoding for a given learning task, which also contributes to poor predictive capabilities. To address these issues, we present  Harvestman , a method that takes advantage of hierarchical relationships among the possible biological interpretations and representations of genomic variants to perform automatic feature learning, feature selection, and model building.    Results  We demonstrate that  Harvestman  scales to thousands of genomes comprising more than 84 million variants by processing phase 3 data from the 1000 Genomes Project, one of the largest publicly available collection of whole genome sequences. Using breast cancer data from The Cancer Genome Atlas, we show that  Harvestman  selects a rich combination of representations that are adapted to the learning task, and performs better than a binary representation of SNPs alone. We compare  Harvestman  to existing feature selection methods and demonstrate that our method is more  parsimonious —it selects smaller and less redundant feature subsets while maintaining accuracy of the resulting classifier.    Conclusion   Harvestman  is a hierarchical feature selection approach for supervised model building from variant call data. By building a knowledge graph over genomic variants and solving an integer linear program ,  Harvestman  automatically and optimally finds the right encoding for genomic variants. Compared to other hierarchical feature selection methods,  Harvestman  is faster and selects features more parsimoniously.

Harvestman: a framework for hierarchical feature learning and selection from whole genome sequencing data