Sofia Khan

This paper provides consensus recommendations for standardizing bioinformatics practices in clinical whole genome sequencing to ensure accuracy, reproducibility, and comparability of results.

VarSCAT annotates genomic variant sequence contexts, revealing that over 75% of human indels have breakpoint ambiguities and over 80% of STR region variants are indels.

The paper evaluates variant calling tools for indel detection across different NGS datasets, showing tool and sequencing setting impacts on accuracy.

The paper introduces a pipeline to analyze complex local DNA mutations using long-read sequencing and presents a catalog of rearrangements in a human cell line.