create_bwa_index

#summary Create a BWA index from sequences in stream for use with bwa_seq.

Biopiece: create_bwa_index

Description

create_bwa_index creates a BWA index using ´bwa index´ on sequences found in the stream.

BWA must be installed in order for create_bwa_index to work. Read more here:

http://maq.sourceforge.net/bwa-man.shtml

Usage

... | create_bwa_index [options]

Options

[-?          | --help]                  #  Print full usage description.
[-x          | --no_stream]             #  Do not emit records.
[-d <dir>    | --directory=<dir>]       #  Directory to cantain index files.
[-i <string> | --index_name=<string>]   #  Index name.
[-I <file!>  | --stream_in=<file!>]     #  Read input from stream file  -  Default=STDIN
[-O <file>   | --stream_out=<file>]     #  Write output to stream file  -  Default=STDOUT
[-v          | --verbose]               #  Verbose output.

Examples

To create a BWA index from a FASTA file, do:

read_fasta -i <FASTA file(s)> | create_bwa_index -d ~/my_dir -i my_index -x

You will then get the following files:

~/my_dir/my_index.ann
~/my_dir/my_index.bwt
~/my_dir/my_index.pac
~/my_dir/my_index.rbwt
~/my_dir/my_index.rpac
~/my_dir/my_index.rsa
~/my_dir/my_index.sa

And finally to use this new index with bwa_seq, simply do:

read_fasta -i <FASTA file(s)> | bwa_seq -i ~/my_dir/my_index

See also

read_fasta

bwa_seq

Author

Martin Asser Hansen - Copyright (C) - All rights reserved.

[email protected]

September 2009

License

GNU General Public License version 2

http://www.gnu.org/copyleft/gpl.html

Help

create_bwa_index is part of the Biopieces framework.

http://www.biopieces.org