Question: Does BWA mem work with uBAM file?
0
gravatar for Abdul Rafay Khan
8 months ago by
Karachi, PK
Abdul Rafay Khan880 wrote:

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

align bwa bwa mem ubam • 508 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by Abdul Rafay Khan880
3
gravatar for ATpoint
8 months ago by
ATpoint8.0k
Germany
ATpoint8.0k 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 8 months ago • written 8 months ago by ATpoint8.0k
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