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Fixing BAM file generated without .alt index file during BWA

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.

bwa bam
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updated by Biostar Biostar • written by Hadi M • Hadi M

1 answer

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.

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written by ATpoint ATpoint

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

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written by Hadi M • Hadi M

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

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written by ATpoint ATpoint

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