andygxzeng/ECSI: Espresso - Somatic Mutation Calling using Contextual Error Models

Traditional variant calling methods utilize variant allele frequency (VAF) cutoffs to call variants. These cutoffs are often set arbitrarily and the measure becomes problematic when trying to call at variants at low VAFs, where true biological variation becomes hard to distinguish from sequencing error. The 'Espresso' package employs a novel variant calling approach that models sequencing error distributions across 192 trinucleotide contexts and conducts variant calling by comparing each putative variant to its corresponding contextual error distribution. This demonstrates superior sensitivity and specificity over existing variant calling methods and bolsters our ability to accurately distinguish signal from noise at very low VAFs.

install.packages("remotes")
remotes::install_github("andygxzeng/ECSI")