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

NAME

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

SYNOPSIS

samtools flags FLAGS...

DESCRIPTION

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

AUTHOR

Written by Petr Danacek from the Sanger Institute.

SEE ALSO

samtools(1)

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

15 April 2024 samtools-1.20