Meerkat
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Application data |
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| Biological application domain(s) | Structural variation |
|---|---|
| Technology | Illumina |
| Maintained? | Maybe |
| Input format(s) | BAM |
Summary: Meerkat is designed to identify structure variations (SVs) from paired end high throughput sequencing data.
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Description
Meerkat is designed to identify structure variations (SVs) from paired end high throughput sequencing data. It predicts SVs from discordant read pairs (pairs that mapped to reference genome in unexpected way). Then it looks for reads that cover the predicted breakpoints junctions (split read support), refines breakpoints by local alignments and predicts mechanisms that SVs are formed. It is more sensitive, with remapping of unmapped and partially mapped reads, especially when the insert size of sequencing library is small (i.e. read lenght of 100bp and insert size is 200bp), since the SV breakpoint has to be inbetween the paired end reads to form discordant read pair. With discordant read pair, split read support and some filtering steps, it has low false positive rate. It can also take into account of reads from repetitive regions (non-uniquely mapped), combine discordant read pair clusters to predict complex events, and select the most supported and smallest events.
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References
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