muCNV: Genotyping Structural Variants for Population-level Sequencing.

Goo Jun
Fritz Sedlazeck
Qihui Zhu, The Jackson Laboratory
Adam English
Ginger Metcalf
Hyun Min Kang
Human Genome Stuctural Variation Consortium
Charles Lee, The Jackson Laboratory
Richard Gibbs
Eric Boerwinkle


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.

AVAILABILITY: muCNV is publicly available for download at:

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.