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Add clipping heuristic to indel realigner #63

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fnothaft opened this Issue Jan 27, 2014 · 1 comment

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fnothaft commented Jan 27, 2014

Currently, the indel realigner code unclips all reads when locally realigning. This is OK (we won't wind up with worse alignments) but we may be missing out on the opportunity to realign some reads. I believe that we could have a clipping heuristic that would improve this—something like whether the base was previously clipped and has a low quality score.

@fnothaft fnothaft added the wontfix label Jul 20, 2016

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fnothaft Jul 20, 2016

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Closing as won't fix. We will probably EOL the indel realigner post 1.0.0.

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fnothaft commented Jul 20, 2016

Closing as won't fix. We will probably EOL the indel realigner post 1.0.0.

@fnothaft fnothaft closed this Jul 20, 2016

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