.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH BAMTOFASTQ.PY "1" "June 2020" "bamtofastq.py 0.0.1+git20170413.ccd079d" "User Commands"
.SH NAME
bamtofastq.py \- Convert a coordinate sorted BAM file to FASTQ
.SH SYNOPSIS
.B bamtofastq.py
[\-h] [\-r STR] [\-n] [\-S] [\-H FILE] [BAM [BAM ...]]
.SH DESCRIPTION
Convert a coordinate sorted BAM file to FASTQ
(ignores unpaired reads)
.SH OPTIONS
.SS "positional arguments:"
.TP
BAM
Input BAM file(s). If absent then defaults to stdin.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-r\fR STR, \fB\-\-readgroup\fR STR
Read group(s) to extract (comma separated)
.TP
\fB\-n\fR, \fB\-\-rename\fR
Rename reads
.TP
\fB\-S\fR, \fB\-\-is_sam\fR
Input is SAM format
.TP
\fB\-H\fR FILE, \fB\-\-header\fR FILE
Write BAM header to file
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.