Does BWA mem work with uBAM file?
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4.8 years ago

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

uBAM bwa bwa mem align • 3.2k views
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4.8 years ago
ATpoint 66k

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.

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