NAME

bamtofastq.py - Convert a coordinate sorted BAM file to FASTQ

SYNOPSIS

bamtofastq.py [-h] [-r STR] [-n] [-S] [-H FILE] [BAM [BAM ...]]

DESCRIPTION

Convert a coordinate sorted BAM file to FASTQ (ignores unpaired reads)

OPTIONS

positional arguments:

BAM
Input BAM file(s). If absent then defaults to stdin.

optional arguments:

-h, --help
show this help message and exit
-r STR, --readgroup STR
Read group(s) to extract (comma separated)
-n, --rename
Rename reads
-S, --is_sam
Input is SAM format
-H FILE, --header FILE
Write BAM header to file

AUTHOR


This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.