Any option in bwa mem aligner for headless sam output?

Question

[robjohn70000]

Hi,

In the bowtie2 implementation for read alignment to a reference, there is an option (--no-sq Suppress @SQ SAM header lines.) to obtain a headless sam file as output. I want to carry out alignments using bwa mem and obtain headless sam file as ouput. I have checked the bwa mem manual for an quivalent flag and couldn't find any. Any ideas?

Thanks

Answer 1

[Pierre Lindenbaum]

bwa mem ref.fa R1.fq.gz R2.fq.gz | grep -v '^@SQ'

[robjohn70000]

Thanks so much @Pierre Lindenbaum