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.

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