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create_bwa_index
Martin Asser Hansen edited this page Oct 2, 2015
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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
... | create_bwa_index [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.
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
Martin Asser Hansen - Copyright (C) - All rights reserved.
September 2009
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
create_bwa_index is part of the Biopieces framework.