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Novelty was identified by comparing the breakpoints with 50% reciprocal overlap criterion.
To annotate whether the SVs called from GRCh37 were also shared with GRCh38 SV sets, we compared each AK1 breakpoints with 50% reciprocal overlap criterion.
Using the "40% either" overlap criterion instead of the "any" overlap criterion increases these numbers only slightly (Table 1).
Using the "40% either" overlap criterion resulted in a slightly higher number of novel CNVs (Table 6).
For each iteration or each simulated dataset, we compared the number of CNVs detected with the true CNV list by 1 bp overlap criterion.
Using HMMSeg alone with the "any" overlap criterion, we found two novel CNVs (both gains) in schizophrenia subjects (supplemental Figure S6), whereas using only cnvPartition with a 3-probe minimum with the "any" overlap criterion, we found three novel CNVs (all losses) in schizophrenia subjects (supplemental Figure S7).
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Predictions by symmetry overlap criteria and the edge-to-edge model were also compared to observations.
We demonstrate that the choice of algorithm and overlap criteria affects how many (if any) CNVs are found that have not been previously reported in the literature.
However, after merging CNVs across individuals and between studies, only 6,735 unique CNVs (i.e., CNVRs) exist when applying the "any" overlap criteria (Table 1).
If it did not meet the overlap criteria for all CNV calls currently assigned to any of the previously designated CNV loci, it was assigned to a new CNV locus.
Counts are the number of reads that align to each annotated region (based on a user-definable overlap criteria).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com