bamtofastq.py - Convert a coordinate sorted BAM file to FASTQ

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.

bamtofastq.py 0.0.1+git20170413.ccd079d             June 2020                                   BAMTOFASTQ.PY(1)

       Convert a coordinate sorted BAM file to FASTQ (ignores unpaired reads)

       bamtofastq.py - Convert a coordinate sorted BAM file to FASTQ

positionalarguments:
       BAM    Input BAM file(s). If absent then defaults to stdin.

   optionalarguments:-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

bamtofastq.py [-h] [-r STR] [-n] [-S] [-H FILE] [BAM [BAM ...]]