.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH BAMGROUPREADS.PY "1" "June 2020" "bamgroupreads.py 0.0.1+git20170413.ccd079d" "User Commands"
.SH NAME
bamgroupreads.py \- Group BAM file by read IDs without sorting
.SH SYNOPSIS
.B bamgroupreads.py
[\-h] [\-i BAM] [\-r STR] [\-d] [\-f] [\-S] [\-b] [\-u] [\-M]
.SH DESCRIPTION
Group BAM file by read IDs without sorting
.SH OPTIONS
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-i\fR BAM, \fB\-\-input\fR BAM
Input BAM file
.TP
\fB\-r\fR STR, \fB\-\-readgroup\fR STR
Read group(s) to extract (comma separated)
.TP
\fB\-d\fR, \fB\-\-reset_dups\fR
Reset duplicate flags
.TP
\fB\-f\fR, \fB\-\-fix_flags\fR
Fix mate flags for secondary reads
.TP
\fB\-S\fR
Input is SAM format
.TP
\fB\-b\fR
Output BAM format
.TP
\fB\-u\fR
Output uncompressed BAM format (implies \fB\-b\fR)
.TP
\fB\-M\fR
split reads are flagged as secondary, not supplementary. For compatibility with legacy BWA\-MEM "\-M" flag
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.