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/>