AB Large Indel Tool
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Application data |
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| Created by | ABI |
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| Biological application domain(s) | Indel detection, Sequencing |
| Principal bioinformatics method(s) | Mapping |
| Technology | ABI SOLiD |
| Created at | ABI |
| Maintained? | No |
| Input format(s) | CMAP |
| Output format(s) | GFF |
| Programming language(s) | Perl |
| Licence | GPL |
| Operating system(s) | Linux 64 |
Summary: Identifies deviations in clone insert size that indicate intra-chromosomal structural variations compared to a reference genome.
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This software identifies deviations in clone insert size that indicate intra-chromosomal structural variations compared to a reference genome. Insertions and deletions (indels) up to 100Kb are inferred by identifying positions in the genome in which the pairing distance between mapped mate pairs is significantly deviated from what is expected at the given level of clone coverage. A look-up table is created in which the amount that the clones must be deviated to achieve one standard deviation of significance is the standard error at each level of clone coverage. This produces an asymptotic curve in which the minimum size of detectable indels at a given level of significance drops rapidly as the clone coverage increases. The look-up table is used to determine the significance of the deviation in average insert size at each position in the genome. Regions of the genome that are significantly deviated are selected as candidate indels and hierarchical clustering is used to segregate the clones into groups in which the difference in the sizes of all clones in a group is less than the range specifiied by the user. Clusters with too few clones (as specified by the user) are removed and the candidates are assessed to determine if there remains a homozygous or heterozygous population of deviated insert sizes. All clones deviated by ≥ 100 kb are discarded. Clones from various libraries with various insert sizes contribute to a single indel call by combining the probabilities associated with the clones from each library
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