Manual page from samtools-1.19
released on 12 December 2023


samtools flags – convert between textual and numeric flag representation.


samtools flags FLAGS...


Convert between textual and numeric flag representation.

Each FLAGS argument may be either an integer (in decimal, hexadecimal, or octal) representing a combination of the listed numeric flag values, or a comma-separated string NAME,...,NAME representing a combination of the flag names listed below.


0x1PAIREDpaired-end (or multiple-segment) sequencing technology
0x2PROPER_PAIReach segment properly aligned according to the aligner
0x4UNMAPsegment unmapped
0x8MUNMAPnext segment in the template unmapped
0x10REVERSESEQ is reverse complemented
0x20MREVERSESEQ of the next segment in the template is reverse complemented
0x40READ1the first segment in the template
0x80READ2the last segment in the template
0x100SECONDARYsecondary alignment
0x200QCFAILnot passing quality controls
0x400DUPPCR or optical duplicate
0x800SUPPLEMENTARYsupplementary alignment


Written by Petr Danacek from the Sanger Institute.


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