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Left right aligning hides repeat information #18

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jamescasbon opened this Issue Oct 12, 2011 · 1 comment

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I have a putative insert that is probably an artifact of 454 data. I would like to filter it based on the repeat flag.
The indel is TG(4)C/TG(5)C.

If I do not left right align, I get this SNP:

chr22   42525351        .       G       GG  REPEAT=G:4

Which is all good. If I do left right realign I get:

chr22   42525347        .       T       TG

With no repeat flag. This makes it harder to filter this kind of artifact. Presumably this is because the new location of the indel (the T base) is not part of the repeat.

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ekg commented Oct 2, 2013

This is very interesting. Unfortunately, I've not been maintaining this functionality. Are you still using it?

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