MuCNV: Genotyping structural variants for population-level sequencing

Abstract

Motivation: There are high demands for joint genotyping of structural variations with short-read sequencing, but efficient and accurate genotyping in population scale is a challenging task. Results: We developed muCNV that aggregates per-sample summary pileups for joint genotyping of >100 000 samples. Pilot results show very low Mendelian inconsistencies. Applications to large-scale projects in cloud show the computational efficiencies of muCNV genotyping pipeline. Availabilityand implementation: muCNV is publicly available for download at: https://github.com/gjun/muCNV.