VAAL - Variant Ascertainment Algorithm | Tool name | VAAL - Variant Ascertainment Algorithm |
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| URL | http://www.mybiosoftware.com/sequence-analysis/1246 |
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| Important features | 1. A variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex genetic variants. High sensitivity on bacterial data sets.
2. Compare reads from one strain to a reference sequence from another strain.
3. Compare reads from two strains to each other, using a third strain to determine homology. |
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| Citations | Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, Warren RM, Hung DT, Birren BW, Lander ES, Jaffe DB. Sensitive, specific polymorphism discovery in
bacteria using massively parallel sequencing. Nat Methods. 2009 Jan;6(1):67-9. Epub 2008 Dec 14. PubMed PMID: 19079253; PubMed Central PMCID: PMC2613166. |
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| Year of publication | 2009 |
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| Rank by usage frequency | 100 |
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| Function | Alignment/Mapping, SNP discovery, Indel discovery, Structural variant discovery |
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| Category | Downloadable |
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| Input file format | FASTA &.qual |
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