Question: Does BWA mem work with uBAM file?
0
gravatar for Abdul Rafay Khan
9 weeks ago by
Karachi, PK
Abdul Rafay Khan790 wrote:

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

align bwa bwa mem ubam • 173 views
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by Abdul Rafay Khan790
2
gravatar for ATpoint
9 weeks ago by
ATpoint3.5k
Germany
ATpoint3.5k 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 9 weeks ago • written 9 weeks ago by ATpoint3.5k
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