CoNIFER uses Exome sequencing data to find CNV and genotype the copy-number of duplicated genes. As exome capture reactions are subject to strong and systematic capture biases between sample batches, we implemented Singular value decomposition (SVD) to eliminate these biases in exome data.
It is to detect rare population-level variants. It's not for CNA.
- Python 2.7 above and Python 3 is not supported yet.
- NumPy: vector calculation
- PyTables: data store in HDF5
- pysam: BAM file parsing
- matplotlib: Duplication/deletion region visualization
- Create RPKM values for all samples BAM
- Analyze all RPKM values for all samples and create SVD-ZRPKM values.
- Call CNV by SVD-ZRPKM
- Visualize CNV region
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