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Variable Non-Overlapping Window CBS and HMM Intersect (VNOWCHI): A Copy Number Variant Calling Pipeline

VNOWCHI is a copy number variant calling pipeline that utilizes the Circular Binary Segmentaion and Hidden Markov Model algorithms. It has been used to determine the ploidy and sex status of embryos:

Daughtry, B. L., Rosenkrantz, J. L., Lazar, N. H., Fei, S. S., Redmayne, N., Torkenczy, K. A., Adey, A., Gao, L., Park, B., Nevonen, K.A., Carbone, L., Chavez, S. L. (2019). Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion. Genome Research, 29(3), 367-382. doi:10.1101/gr.239830.118