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  • Last update: 5 years ago
  • Total downloads: 65
  • Operating system: Win All
  • Publisher: Niklas Krumm
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windows default iconCoNIFER Publisher's description

CoNIFER uses exome sequencing data to find copy number variants

CoNIFER uses exome sequencing data to find copy number variants (CNVs) 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. CoNIFER offers the ability to mix exome sequence from multiple experimental runs by eliminating batch biases. Together with a short read aligner such as mrsFAST which can align reads to multiple locations, CoNIFER can robustly detect rare CNVs and estimate the copy number of duplicated genes up to ~8 copies with current exome capture kits. To get started right away, read the quick start guide.

System Requirements:

В· Python
В· NumPy
В· pysam (optional)
В· matplotlib (optional)
Program Release Status: New Release
Program Install Support: Install and Uninstall


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