bamtofastq.py1
Convert a coordinate sorted bam file to fastq
Usage
bamtofastq.py [-h]
[-r
STR]
[-n]
[-S]
[-H
FILE]
[BAM
[BAM ...]]
Overview
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