VARIANT CALLER
Processes and systems for reading variants from a genome sample relative to a reference genomic sequence are provided. An exemplary process includes collecting a set reads and generating a k-mer graph from the reads. For example, the k-mer graph can be constructed to represent all possible substring...
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| creator | HAQUE IMRAN SAEEDUL MAGUIRE JARED ROBERT GIBIANSKY ANDREW LEONIDOVICH ROBERTSON ALEXANDER DE JONG |
| description | Processes and systems for reading variants from a genome sample relative to a reference genomic sequence are provided. An exemplary process includes collecting a set reads and generating a k-mer graph from the reads. For example, the k-mer graph can be constructed to represent all possible substrings of the collected reads. The k-mer graph may be reduced to a contiguous graph, and a set of possible haplotypes generated from the contiguous graph. The process may further generate, the error table providing a filter for common sequencer errors. The process may then generate a set of diplotypes based on the set of haplotypes and the generated error table and score the set of diplotypes to identify variants from the reference genome. Scoring the diplotypes may include determining a posterior probability for each of the diplotypes, with the highest scoring diplotype(s) reported as the result. |
| format | Patent |
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| subjects | CALCULATING COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS COMPUTING COUNTING INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS PHYSICS |
| title | VARIANT CALLER |
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