How to convert bwa mem output to BAM format without saving SAM file

Question

I want to go straight from bwa mem alignment to BAM format as I don't need the SAM file and it takes up too much space. How do I achieve this?

Wouter De Coster · Accepted Answer · 2018-06-09 08:28:19Z

27

For directly outputting a sorted bam file you can use the following:

bwa mem genome.fa reads.fastq | samtools sort -o output.bam -

Optionally using multiple threads:

bwa mem -t 8 genome.fa reads.fastq | samtools sort -@8 -o output.bam -

answered May 12, 2017 at 7:28

Wouter De Coster

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$\begingroup$ Ah, great solution if sorting is needed! I had tried this in the past but I was trying to pipe it though samtools view and then into sort. Didn't realise you could go straight into sort. $\endgroup$
– Michael Hall
May 12, 2017 at 23:48

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Michael Hall · Accepted Answer · 2017-09-11 05:33:52Z

12

Found the solution. You just need to pipe the output from bwa mem into samtools view like so

bwa mem ref.fa in.fq | samtools view -bS - > out.bam

The - in samtools view tells it to read from stdin.

answered May 12, 2017 at 5:08

Michael Hall

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$\begingroup$ In my workflow, BWA output goes to MergeBamAlignment, so samtools view seemed lower overhead than samtools sort. (Directly piping from BWA to MergeBamAlignment, as suggested here, failed for me.) $\endgroup$
– Ulrich Stern
Feb 1 at 18:53

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2 Answers 2