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

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,

alignment bwa-mem

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updated 4.1 years ago by GenoMax

• written 4.1 years ago by Qboy •

See: bwa mem on a bam file

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written 4.1 years ago by GenoMax

2 answers

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

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written 4.1 years ago by swbarnes2

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

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

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written 4.1 years ago by draccident •

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