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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/>
| 21 February 2022 | samtools-1.15 |
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