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 · 2018-06-09T08:28:19.713

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 -

edited Jun 09 '18 at 08:28

answered May 12 '17 at 07:28

Wouter De Coster

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. – Michael Hall May 12 '17 at 23:48

Michael Hall · Answer 2 · 2017-09-11T05:33:52.847

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.

edited Sep 11 '17 at 05:33

answered May 12 '17 at 05:08

Michael Hall

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.) – Ulrich Stern Feb 01 '23 at 18:53

2 Answers2