Does BWA mem work with uBAM file?

Question

[Abdul Rafay Khan]

I want to align my uBAM files using bwa mem. Does BWA mem works with uBAM files?

Answer 1

[ATpoint]

No, you'll have to convert to fastq. Options are e.g. bedtools bamtofastq or samtools fastq. Picard has a command for this too but I never used it. You could avoid writing the bam to fastq on disk, if you use a simple pipe solution. This blog entry provides some inspiration on that.