DOKK / manpages / debian 12 / bamkit / bamgroupreads.py.1.en
BAMGROUPREADS.PY(1) User Commands BAMGROUPREADS.PY(1)

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

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

Group BAM file by read IDs without sorting

show this help message and exit
Input BAM file
Read group(s) to extract (comma separated)
Reset duplicate flags
Fix mate flags for secondary reads
Input is SAM format
Output BAM format
Output uncompressed BAM format (implies -b)
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.

June 2020 bamgroupreads.py 0.0.1+git20170413.ccd079d