BWA MEM/Can BWA use bam file to re-align it to the new ref.fa?

Question

[Qboy]

Hey, community!

I have a question. Can BWA-MEM use BAM/CRAM file and re-align to the new reference genome? I would be glad if you could share your full script on this. I could not find any information on the internet.

Thank you,

[GenoMax]

See: bwa mem on a bam file

Answer 1

[swbarnes2]

The old bwa aln function has an option to take a bam as input, but it doesn't look like bwa mem does.

Answer 2

[draccident]

BWA is designed to take Illumina read data and align it to a reference, not Bams.

http://bio-bwa.sourceforge.net/bwa.shtml