Is it possible to convert bam files with different parameters?

Question

[octpus616]

I recently obtained some bam files of WGS data. However, the trouble is that these bam files are mapped with the -M parameter, which is incompatible with the software I need for the next analysis. Is there any way to get it out without re-mapping (-M Parameter)?

Best
Zhang

[Ram]

Hello a661881!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/15019/is-it-possible-to-convert-bam-files-with-different-parameters

This is typically not recommended as it runs the risk of annoying people in both communities.

[octpus616]

oh，I am sorry for that, I am too eager to ask for answers, I will pay attention to these rules next time.

Answer 1

[ATpoint]

Nope, remapping is the only option afaik. I had the same problem in the past and recall that I did not find a reliable converter to "undo" the -M option of bwa, so it was more efficient and reliably to just remap the whole thing.