Question: Does BWA mem work with uBAM file?
0
gravatar for Abdul Rafay Khan
10 months ago by
Karachi, PK
Abdul Rafay Khan890 wrote:

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

align bwa bwa mem ubam • 637 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by Abdul Rafay Khan890
3
gravatar for ATpoint
10 months ago by
ATpoint11k
Germany
ATpoint11k 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 10 months ago • written 10 months ago by ATpoint11k
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