Tobias Marschall

This paper introduces a latent variable model to improve sensitivity and control false discovery rate in somatic indel discovery, showing significant improvements in recall for deletions.

This paper introduces DIGTYPER, a statistical method for genotyping inversions and duplications from NGS data, showing improved performance over DELLY for duplications and short inversions.

Re-aligning reads to both alleles gives WhatsHap the lowest PacBio switch error rates (full coverage: 0.24% real, 0.02% simulated) and better indel phasing than hapCUT and phASER.

This paper reviews computational pan-genomics, discussing its status, potential, and challenges across multiple biological disciplines.

The paper introduces a heuristic algorithm to select reads for haplotype assembly, improving connectivity and correct variant phasing compared to random selection in WhatsHap.

This paper combines read-based phasing and genetic haplotyping to improve haplotype inference in related individuals, achieving higher accuracy and more phased variants than either method alone.