Fixing BAM file generated without .alt index file during BWA

Question

[Hadi M]

Hi everyone,

I generated a BAM file after aligning my NGS reads against the reference genome using BWA. My reference genome contains ALT contigs but I did not supply the .alt index file during alignment. I know I can just do the alignment again with the .alt index file but before I proceed to that, I am curious if there are any tools that can correct the alignment information in the BAM file as if I supplied the .alt index file during alignment.

Many thanks.

Answer 1

[ATpoint]

I am not aware of any solution for this. I would realign. Be sure to use the ALT-aware version of bwa via bwa-kit when including ALT into the reference.

[Hadi M]

Yeah seems like there's no way to fix the BAM file as of now so I have to realign my reads. Cheers.

[ATpoint]

It is also safer to start from scratch if this is possible. Custom filtering is hard to reproduce at times.