1samtools-flags(1) Bioinformatics tools samtools-flags(1)
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6 samtools flags - convert between textual and numeric flag representa‐
7 tion.
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10 samtools flags FLAGS...
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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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38 Written by Petr Danacek from the Sanger Institute.
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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)