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.