ekg/freebayes — Issue #18: Left right aligning hides repeat information
Author: jamescasbon
Created: 2011-10-12 10:28:23+00:00
State: open

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.