samtools flag 1548

Hi all,

Just a quick question- can somebody please explain to me what is the meaning of 1548 in the following samtools command:

samtools view -b -F 1548

Thanks, RT

samtools bitwise flags

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updated 9.5 years ago by Pierre Lindenbaum

• written 9.5 years ago by GR

1 answer

see https://broadinstitute.github.io/picard/explain-flags.html . samtools only include reads with none of the property set in the sam flag:

read unmapped
mate unmapped
read fails platform/vendor quality checks
read is PCR or optical duplicate

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written 9.5 years ago by Pierre Lindenbaum

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