samtools-flags - Man Page
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 website: <http://www.htslib.org/>
Referenced By
samtools(1), samtools-ampliconstats(1), samtools-bedcov(1), samtools-depth(1), samtools-view(1).
7 April 2022 samtools-1.15.1 Bioinformatics tools