1samtools-flags(1)            Bioinformatics tools            samtools-flags(1)
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NAME

6       samtools  flags  - convert between textual and numeric flag representa‐
7       tion.
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SYNOPSIS

10       samtools flags FLAGS...
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DESCRIPTION

14       Convert between textual and numeric flag representation.
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16       Each FLAGS argument may be either an integer (in decimal,  hexadecimal,
17       or octal) representing a combination of the listed numeric flag values,
18       or a comma-separated string NAME,...,NAME representing a combination of
19       the flag names listed below.
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21       FLAGS:
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23         0x1   PAIRED          paired-end (or multiple-segment) sequencing technology
24         0x2   PROPER_PAIR     each segment properly aligned according to the aligner
25         0x4   UNMAP           segment unmapped
26         0x8   MUNMAP          next segment in the template unmapped
27        0x10   REVERSE         SEQ is reverse complemented
28        0x20   MREVERSE        SEQ of the next segment in the template is reverse complemented
29        0x40   READ1           the first segment in the template
30        0x80   READ2           the last segment in the template
31       0x100   SECONDARY       secondary alignment
32       0x200   QCFAIL          not passing quality controls
33       0x400   DUP             PCR or optical duplicate
34       0x800   SUPPLEMENTARY   supplementary alignment
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AUTHOR

38       Written by Petr Danacek from the Sanger Institute.
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SEE ALSO

42       samtools(1)
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44       Samtools website: <http://www.htslib.org/>
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48samtools-1.13                     7 July 2021                samtools-flags(1)