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]

Group BAM file by read IDs without sorting

-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

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