VAAL
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Application data |
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| Biological application domain(s) | Structural variation, SNP detection, Indel detection |
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| Principal bioinformatics method(s) | Sequence alignment |
| Created at | Broad Institute |
| Maintained? | Maybe |
Summary: VAAL is a variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex genetic variants.
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On bacterial data sets, VAAL achieves very high sensitivity, and near perfect specificity. VAAL can be used to compare reads from one strain to a reference sequence from another strain. It can also be used to compare reads from two strains to each other, using a third strain to determine homology. For example, we have used VAAL to find a single mutation responsible for bacterial resistance: the output of the program was that single mutation and no others. VAAL uses an assisted assembly algorithm that borrows from ALLPATHS.
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