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How to compare PennCNV calls with other algorithms?

April 26, 2017algorithms compare penncnv

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How to compare PennCNV calls with other algorithms?

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If a user also generates CNV calls by cnvPartition or QuantiSNP in BeadStudio/GenomeStudio, you can export the CNV calls to a XML file (see illustration described in this tutorial), then use the convert_cnv.pl program (with “-intype xml -outtype penncnv” argument) to convert the XML file to PennCNV format. If a user also generates CNV calls by Birdseye program, the convert_cnv.pl program can also convert BirdSeed calls to standard PennCNV format. Next, you can use the compare_cnv.pl program (use -m argument to read the manual) to compare the CNV calls generated by different programs that are all in PennCNV format. A two-column list file should be prepared that specifies the file name correspondence in PennCNV call file and the call file generated by the other algorithm (but converted to PennCNV format).