Michael F. Lin

The paper introduces a scalable variant-calling method using DeepVariant and GLnexus, achieving improved quality and cost savings over existing practices.

The paper introduces spVCF, a compressed variant call format that reduces file size by over 10X with minimal information loss.

IDseq provides a cloud-based metagenomics pipeline for pathogen detection, enabling analysis of mNGS data with tools for taxonomic assignment and novel pathogen identification.

The paper introduces vg, a toolkit for creating and using variation graphs as genome references, improving read mapping and variant calling accuracy over linear references.

GLnexus, a joint variant caller backed by an incrementally growable gVCF database, largely matched GATK on 50,000 exomes while keeping more rare indels and using 3.8–6.6-fold fewer core-hours.

This paper introduces genome graphs as an alternative to linear reference genomes, showing they improve read mapping and variant calling compared to the standard GRCh38 reference.