Any option in bwa mem aligner for headless sam output? · Biostar

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Any option in bwa mem aligner for headless sam output?

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

sam bowtie2 bwa alignment

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updated 3.9 years ago by Pierre Lindenbaum

• written 3.9 years ago by robjohn70000

1 answer

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

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written 3.9 years ago by Pierre Lindenbaum

Thanks so much @Pierre Lindenbaum

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written 3.9 years ago by robjohn70000

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