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Tool for identifying INDELs and Tandem duplication break points

Does anyone know of a tool to help identify break points of various structural variants such as insertions, deletions, and tandem duplications?

I was looking at BreakSeek but it lacks the identification of tandem duplications. There was also DB2 and ITD assembler but they don't support insertions or deletions. Ideally the tool would encompass all SVs mentioned above.

DELLY was a potential contender until I saw it severely lacked sensitivity for insertions as well as small deletions.

Thanks for your help!

svs

I think I'm going to choose a combination of BreakSeek and ITD assembler should another option not be found.

I have been testing Strelka and Pindel lately for indels, though I have not gotten too far in assessing the results.

Please scan the literature for recent benchmarking papers. Lumpy, SoftSV, Manta, many other tools out there. Please use google and PubMed.

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