Tool for identifying INDELs and Tandem duplication break points

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4.8 years ago

swissman.howard97 • 0

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 • 1.0k views

ADD COMMENT • link updated 10 months ago by Ram 43k • written 4.8 years ago by swissman.howard97 • 0

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

ADD REPLY • link 4.8 years ago by steve ★ 3.5k

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

ADD REPLY • link 4.8 years ago by swissman.howard97 • 0

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