BAMTOFASTQ.PY

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.