muCNV: genotyping structural variants for population-level sequencing

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.

Automated summary

This study introduces muCNV, a software developed for joint genotyping of over 100,000 samples, showing high efficiency and accuracy in population-scale genotyping. Pilot results demonstrate very low Mendelian inconsistencies, with computational efficiencies highlighted when applied to large-scale projects in the cloud.