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: https://github.com/gjun/muCNV.
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