Worthwhile to upgrade BWA in NGS pipeline?

Question

[BCArg]

We are currently using BWA (v0.7.10) as the aligner algorithm in our NGS pipeline. To summarise, we perform whole genome sequencing (WGS), whole exome sequencing (WES) and sequencing of specific gene panels (e.g. human mendeliomes) mostly using Novaseq.

We are now wondering whether it is worthwhile to update our BWA version to the most up-to-date one (v.0.7.17) in our pipeline. As the BWA aligner is part of a whole pipeline, the benefits from a possible upgrade should outweigh the risks and time spent for the including a new version in our pipeline.

Has anyone recently upgraded/ been upgrading the BWA algorithm in the pipelines and would have an opinion on that? Like for most of bioinformaticians, we are always trying to find the best compromise between speed and accuracy and I was wondering whether the updated versions show any improvement on those parameters or not really?

Thanks in advance.

Answer 1

[ATpoint]

There have been some minor big bug fixes according to the Github release history. I do not see any point why you would not update it. The command line parameter are exactly the same. The only major difference is that with the newer versions, you can do ALT-aware mapping.