samtools-flags - convert between textual and numeric flag representation.

       Written by Petr Danacek from the Sanger Institute.

       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.

       FLAGS:0x1   PAIRED          paired-end (or multiple-segment) sequencing technology
         0x2   PROPER_PAIR     each segment properly aligned according to the aligner
         0x4   UNMAP           segment unmapped
         0x8   MUNMAP          next segment in the template unmapped
        0x10   REVERSE         SEQ is reverse complemented
        0x20   MREVERSE        SEQ of the next segment in the template is reverse complemented
        0x40   READ1           the first segment in the template
        0x80   READ2           the last segment in the template
       0x100   SECONDARY       secondary alignment
       0x200   QCFAIL          not passing quality controls
       0x400   DUP             PCR or optical duplicate
       0x800   SUPPLEMENTARY   supplementary alignment

       samtools-flags - convert between textual and numeric flag representation.

samtools(1)

       Samtools website: <http://www.htslib.org/>

samtools-1.21                                   12 September 2024                              samtools-flags(1)

       samtools flags FLAGS...