samtools flag 1548

Question

[GR]

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

Answer 1

[Pierre Lindenbaum]

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