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===Motivation=== We are using the VarBin method from CSHL (Baslan et al., Nature Protocols, 2012) to call CNVs in single nuclei. Briefly, artificially generated 36 base reads from every position of hg38 (~3 billion reads) were mapped back to hg38 using Bowtie (-n 2 -e 70 -m 1). Only uniquely aligning reads were retained (~85%); no multiple alignments were considered. Bin boundaries were defined such that all bins have equal expected coverage from a genome with no CNVs. We know that even under ideal conditions, a uniform genome will still display non-diploid copy numbers in certain bins, called "bad bins". These are largely due to incomplete assembly of repetitive regions, such that these regions appear unique in the reference. This leads to a systematic bias which can be profiled empirically and corrected.
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