A convention for BEDPE breakpoint positions about svtools HOT 11 CLOSED

@ernfrid is it ok to link your Gist here?

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reference #46

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Definitely. Clearly need to go over all this code more.

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Notes on SV representation

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Also, talked to Ira about this on Friday. He suggested we just mimic VCF, but we didn't have time to discuss in detail.

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I think another pro for LOB is readability; for precise variants, the start/stop of the BEDPE interval are the bases flanking the breakpoint. For example, if an interval is 1 90 91, the breakpoint is between the base at position 90 and the base at position 91.

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^ that would actually be true of ROB, not LOB. but yeah i see your point

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In support of BPT, pairtopair and prune would be the only scripts affected by this scheme. pairToBed would natively support a BPT scheme.

just checking through the pairtopair source, it looks like this modification would be trivially easy, since it would only require internally iterating the position by 1 base.

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BEDPE file definition - http://bedtools.readthedocs.org/en/latest/content/general-usage.html

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I believe we've agreed to the BPT record. #52 is open to address this.

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#52 was merged. Closing this issue.

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