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

NAME
       samtools	 flags	- convert between textual and numeric flag representa-
       tion.

SYNOPSIS
       samtools	flags INT|STR[,...]

DESCRIPTION
       Convert between textual and numeric flag	representation.

       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/>

samtools-1.11		       22 September 2020	     samtools-flags(1)

NAME | SYNOPSIS | DESCRIPTION | AUTHOR | SEE ALSO

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