.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH BAMFIXFLAGS.PY "1" "June 2020" "bamfixflags.py 0.0.1+git20170413.ccd079d" "User Commands"
.SH NAME
bamfixflags.py \- filter readgroup(s) from a BAM file
.SH SYNOPSIS
.B bamfixflags.py
[\-h] [\-i BAM] \fB\-l\fR FILE [\-n INT] [\-S] [\-b] [\-u]
.SH DESCRIPTION
filter readgroup(s) from a BAM file
.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\-l\fR FILE, \fB\-\-lib_info\fR FILE
SVTyper JSON file of library information
.TP
\fB\-n\fR INT
Output first n alignments and quit
.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)
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.