Common CNV Finder is a Python tool that finds similar copy number variant (CNV) regions found within two different genomic datasets. It accepts these datasets as CSV files with columns ['Chrom', 'Start', 'Stop', 'Type', 'P_Value'].
Common CNV Finder removes CNVs based on specific parameters, such as: 1. User-defined minimum CNV length 2. User-defined P-value threshold 3. Inaccurate CNV calls located on 'chrM'.
It then generates an output file containing the CNVs common to both samples based on additional criteria: 1. CNV located on same chromosome 2. CNV is of same type (Deletion or Duplication) 3. CNV start sites are within a user-defined distance of each other (i.e. 25 bp) 4. CNV stop sites are within a user-defined distance of each other.
The output file has the same format as the input and can be exported as a CSV.