Question: Does BWA mem work with uBAM file?
0
gravatar for Abdul Rafay Khan
16 months ago by
Karachi, PK
Abdul Rafay Khan1.0k wrote:

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

align bwa bwa mem ubam • 1.0k views
ADD COMMENTlink modified 16 months ago • written 16 months ago by Abdul Rafay Khan1.0k
3
gravatar for ATpoint
16 months ago by
ATpoint18k
Germany
ATpoint18k wrote:

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.

ADD COMMENTlink modified 16 months ago • written 16 months ago by ATpoint18k
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