Is anyone using Abra for realignment of exome/wgs data? Looks like a nice tool, and paper looks good too. I'd be interested in hearing peoples experience of it.
We've had good results using Abra. Of course, we developed it, so my opinion might be biased :)
We use it extensively for cancer gene panels and exomes. We've not used it heavily for WGS. In our WGS test case, it was necessary to split processing up by chromosome.
There is also now a somatic indel caller that specifically works with Abra realignments. Will post details on this on the Abra website soon.
Just a thought, but... if you align with BBMap, you won't need to realign indels, because they'll be correctly aligned already.
Brian Bushnell This comment is not constructive in its current form. Why would BBMap help? What does BBMap have to do with the original question?
As I understand it, Abra is a tool that takes mapped reads and realigns them around indels, because the reads originating over the indel were not aligned correctly. Locally realigning over suspected indels can help improve alignments, if the mapping (approximate location) is correct. However, it will not place reads on indels if they were mapped somewhere else in the first place, because the mapper could not tolerate long indels and thus did not consider that a valid mapping location. So mapping with a program that cannot tolerate long indels, and subsequently realigning with a tool that can, will generally yield inferior results to mapping and aligning with a single tool that does tolerate long indels... because in the second case, there will be a lower rate of reads being mismapped or left unmapped.
If the goal of the thread is solely to discuss Abra, then my comment is irrelevant. But if the goal is to find tools that do a good job of aligning reads around indels, then it is relevant.
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