NAME

       bamgroupreads.py - Group BAM file by read IDs without sorting

SYNOPSIS

       bamgroupreads.py [-h] [-i BAM] [-r STR] [-d] [-f] [-S] [-b] [-u] [-M]

DESCRIPTION

       Group BAM file by read IDs without sorting

OPTIONS

   optional arguments:
       -h, --help
              show this help message and exit

       -i BAM, --input BAM
              Input BAM file

       -r STR, --readgroup STR
              Read group(s) to extract (comma separated)

       -d, --reset_dups
              Reset duplicate flags

       -f, --fix_flags
              Fix mate flags for secondary reads

       -S     Input is SAM format

       -b     Output BAM format

       -u     Output uncompressed BAM format (implies -b)

       -M     split  reads  are  flagged  as secondary, not supplementary. For compatibility with legacy BWA-MEM
              "-M" flag

AUTHOR

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

bamgroupreads.py 0.0.1+git20170413.ccd079d          June 2020                                BAMGROUPREADS.PY(1)