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.

Requirements

1. Python 2.7 above and Python 3 is not supported yet.
2. NumPy: vector calculation
3. PyTables: data store in HDF5
4. pysam: BAM file parsing
5. matplotlib: Duplication/deletion region visualization

Process

1. Create RPKM values for all samples BAM
2. Analyze all RPKM values for all samples and create SVD-ZRPKM values.
3. Call CNV by SVD-ZRPKM
4. Visualize CNV region

관련논문

• Copy number variation detection and genotyping from exome sequence data Genome Research 2012-05-14

Incoming Links #

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• CNV calling from NGS data

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• An evaluation of copy number variation detection tools from whole-exome sequencing data
• Gene-based comparative analysis of tools for estimating copy number alterations using whole-exome sequencing data

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