bamgroupreads.py

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.