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.