bamgroupreads.py1
Group bam file by read ids without sorting
Usage
bamgroupreads.py [-h]
[-i
BAM]
[-r
STR]
[-d]
[-f]
[-S]
[-b]
[-u]
[-M]
Overview
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