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Mangul-Lab-USC / benchmarking_SV

Updated figures for "A benchmarking of WGS-based structural variant callers" paper
MIT License
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bwa mem flags could be problematic #7

Closed d-cameron closed 3 years ago

d-cameron commented 4 years ago

-a can have a significant impact on caller performance. In the case of GRIDSS, results were signficantly worse when -a was an option.

-Y is similarly problematic: some older callers pre-date the supplementary flag being added to the SAM specifications so essentially require -Y to treat them fairly. Recent callers may actually adhere to the SAM specifications so -Y needs to not be supplied to those callers.

Other callers can rely on specific aligner versions. When I last benchmarked, I found that LUMPY sensitivity got halved due to a minor version change in version of bwa used for alignment.

In summary, -a is a problematic default, and -Y may or may not be required for older callers.

Addicted-to-coding commented 3 years ago

Thanks a lot for your feedback, we have run bwa using the -M option. We have updated our manuscript with this detail.