table of contents
| BAMTOFASTQ.PY(1) | User Commands | BAMTOFASTQ.PY(1) |
NAME¶
bamtofastq.py - Convert a coordinate sorted BAM file to FASTQ
SYNOPSIS¶
bamtofastq.py [-h] [-r STR] [-n] [-S] [-H FILE] [BAM [BAM ...]]
DESCRIPTION¶
Convert a coordinate sorted BAM file to FASTQ (ignores unpaired reads)
OPTIONS¶
positional arguments:¶
- BAM
- Input BAM file(s). If absent then defaults to stdin.
optional arguments:¶
- -h, --help
- show this help message and exit
- -r STR, --readgroup STR
- Read group(s) to extract (comma separated)
- -n, --rename
- Rename reads
- -S, --is_sam
- Input is SAM format
- -H FILE, --header FILE
- Write BAM header to file
AUTHOR¶
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.
| June 2020 | bamtofastq.py 0.0.1+git20170413.ccd079d |