Shane McCarthy

KaryoScan detects chromosomal anomalies from whole-exome sequencing, identifying aneuploidies and complex rearrangements in large cohorts.

BCFtools/csq improves variant consequence prediction by considering haplotype context, correcting 501 compound variants in 1000 Genomes data with faster performance.

The paper compares genome sequences from Finnish and British populations to identify genetic variants enriched in a population bottleneck, finding significant enrichment of rare variants in Finns.

This study uses whole genome sequencing to explore the genetic architecture of inflammatory bowel diseases, identifying a risk variant in ADCY7 for ulcerative colitis but finding limited contribution of low-frequency variants to heritability.

This paper introduces Eagle2, a reference-based phasing algorithm that improves accuracy and speed compared to SHAPEIT2 using the Haplotype Reference Consortium panel.

The paper constructs a haplotype reference panel for genotype imputation, enabling accurate imputation at low minor allele frequencies and enhancing association studies.

This paper introduces a population BWT data structure to efficiently store and analyze sequencing reads from thousands of human genomes, enabling variant calling and viral detection.

The paper analyzes whole-genome sequencing data from Italian founder populations to determine the cause of purging of deleterious variants, concluding that genetic drift and founder effect, not consanguinity, are responsible.