NAME - Convert sequence information from MAF formatted multiple sequence alignment to a BED style annotation format.

SYNOPSIS [options] [file]


-s, --seq-id

Specify the sequence identifier of the sequence which should be used as a reference to create the output. Use for example hg17 if you want to get all sequences containing hg17 in the idenitfier (e.g. hg17.chr10, hg17.chr22,...). If this option is omitted, the first sequence identifier of the first sequence in the first alignment block is used.

-c, --cluster

Combine overlapping alignments and report non-overlapping regions in the BED output.

-v, --version

Prints version information and exits.

-h, --help

Prints a short help message and exits.


Prints a detailed manual page and exits.


This simple programs extracts the position information for a given sequence out of a MAF alignment and outputs it in a BED style annotation format.


 # -s hg17 some.maf

Get the regions of the hg17 sequences in the alignment some.maf.


Stefan Washietl <>