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Added BWA wrapper tool to Short Read Mapping Tools
This commit is contained in:
Kelly Vincent
@@ -0,0 +1,28 @@
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#This is a sample file distributed with Galaxy that enables tools
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#to use a directory of BWA indexed sequences data files. You will need
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#to create these data files and then create a sequence_index_base.loc file
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#similar to this one (store it in this directory ) that points to
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#the directories in which those files are stored. The sequence_index_base.loc
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#file has this format (white space characters are TAB characters):
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#
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#<build> <file_base>
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#
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#So, for example, if you had phiX indexed stored in
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#/depot/data2/galaxy/phiX/base/,
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#then the sequence_index_base.loc entry would look like this:
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#
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#phiX /depot/data2/galaxy/phiX/base/phiX.fa
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#
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#and your /depot/data2/galaxy/phiX/base/ directory
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#would contain phiX.fa.* files:
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#
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#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb
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#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann
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#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt
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#...etc...
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#
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#Your sequence_index_base.loc file should include an entry per line for
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#each index set you have stored. The "file" in the path does not actually
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#exist, but it is the prefix for the actual index files. For example:
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#
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#phiX /depot/data2/galaxy/phiX/base/phiX.fa
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@@ -0,0 +1,28 @@
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#This is a sample file distributed with Galaxy that enables tools
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#to use a directory of BWA indexed sequences data files. You will need
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#to create these data files and then create a sequence_index_color.loc file
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#similar to this one (store it in this directory ) that points to
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#the directories in which those files are stored. The sequence_index_color.loc
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#file has this format (white space characters are TAB characters):
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#
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#<build> <file_base>
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#
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#So, for example, if you had phiX indexed stored in
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#/depot/data2/galaxy/phiX/color/,
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#then the sequence_index_color.loc entry would look like this:
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#
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#phiX /depot/data2/galaxy/phiX/color/phiX.fa
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#
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#and your /depot/data2/galaxy/phiX/color/ directory
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#would contain phiX.fa.* files:
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#
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#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb
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#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann
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#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt
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#...etc...
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#
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#Your sequence_index_color.loc file should include an entry per line for
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#each index set you have stored. The "file" in the path does not actually
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#exist, but it is the prefix for the actual index files. For example:
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#
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#phiX /depot/data2/galaxy/phiX/color/phiX.fa
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@@ -329,8 +329,9 @@
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<tool file="metag_tools/megablast_xml_parser.xml" />
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<tool file="metag_tools/blat_wrapper.xml" />
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<tool file="metag_tools/mapping_to_ucsc.xml" />
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<tool file="sr_mapping/bwa_wrapper.xml" />
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</section>
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<section name="Tracks" id="tracks">
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<tool file="visualization/genetrack.xml" />
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</section>
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</section>
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</toolbox>
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@@ -0,0 +1,119 @@
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#! /usr/bin/python
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"""
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Runs BWA on single-end or paired-end data.
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Produces a SAM file containing the mappings.
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usage: python bwa_wrapper.py reference_sequence indexing_algorithm(is_or_bwtsw) forward_fastq_file reverse_fastq_file(or_None) output alignment_type(single_or_paired) parameters(pre_set_or_full) file_type(solexa_or_solid) file_source(indexed_or_history) maxEditDist fracMissingAligns maxGapOpens maxGapExtens disallowLongDel disallowIndel seed maxEditDistSeed numThreads mismatchPenalty gapOpenPenalty gapExtensPenalty colorSpaceRev suboptAlign noIterSearch outputTopN maxInsertSize maxOccurPairing\nThe last eighteen need to all be specified, or all be None
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"""
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import optparse, os, sys, tempfile
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def stop_err( msg ):
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sys.stderr.write( "%s\n" % msg )
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sys.exit()
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def __main__():
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#Parse Command Line
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parser = optparse.OptionParser()
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parser.add_option('', '--ref', dest='ref', help='The reference genome to use or index')
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parser.add_option('', '--indexingAlg', dest='indexingAlg', help='The algorithm to use while indexing')
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parser.add_option('', '--fastq', dest='fastq', help='The (forward) fastq file to use for the mapping')
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parser.add_option('', '--rfastq', dest='rfastq', help='The reverse fastq file to use for mapping if paired-end data')
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parser.add_option('', '--output', dest='output', help='The file to save the output (SAM format)')
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parser.add_option('', '--genAlignType', dest='genAlignType', help='The type of pairing (single or paired)')
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parser.add_option('', '--params', dest='params', help='Parameter setting to use (pre_set or full)')
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parser.add_option('', '--fileType', dest='fileType', help='Type of reference sequence file (solid or solexa)')
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parser.add_option('', '--fileSource', dest='fileSource', help='Whether to use a previously indexed reference sequence or one form history (indexed or history)')
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parser.add_option('-n', '--maxEditDist', dest='maxEditDist', help='Maximum edit distance if integer')
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parser.add_option('', '--fracMissingAligns', dest='fracMissingAligns', help='Fraction of missing alignments given 2% uniform base error rate if fraction')
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parser.add_option('-o', '--maxGapOpens', dest='maxGapOpens', help='Maximum number of gap opens')
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parser.add_option('-e', '--maxGapExtens', dest='maxGapExtens', help='Maximum number of gap extensions')
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parser.add_option('-d', '--disallowLongDel', dest='disallowLongDel', help='Disallow a long deletion within specified bps')
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parser.add_option('-i', '--disallowIndel', dest='disallowIndel', help='Disallow indel within specified bps')
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parser.add_option('-l', '--seed', dest='seed', help='Take the first specified subsequences')
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parser.add_option('-k', '--maxEditDistSeed', dest='maxEditDistSeed', help='Maximum edit distance to the seed')
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parser.add_option('-t', '--numThreads', dest='numThreads', help='Number of threads')
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parser.add_option('-M', '--mismatchPenalty', dest='mismatchPenalty', help='Mismatch penalty')
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parser.add_option('-O', '--gapOpenPenalty', dest='gapOpenPenalty', help='Gap open penalty')
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parser.add_option('-E', '--gapExtensPenalty', dest='gapExtensPenalty', help='Gap extension penalty')
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parser.add_option('-c', '--colorSpaceRev', dest='colorSpaceRev', help="Reverse query but don't complement it")
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parser.add_option('-R', '--suboptAlign', dest='suboptAlign', help='Proceed with suboptimal alignments even if the top hit is a repeat')
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parser.add_option('-N', '--noIterSearch', dest='noIterSearch', help='Disable iterative search')
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parser.add_option('', '--outputTopN', dest='outputTopN', help='Output top specified hits')
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parser.add_option('', '--maxInsertSize', dest='maxInsertSize', help='Maximum insert size for a read pair to be considered mapped good')
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parser.add_option('', '--maxOccurPairing', dest='maxOccurPairing', help='Maximum occurrences of a read for pairings')
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(options, args) = parser.parse_args()
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# index if necessary
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if options.fileSource == 'history':
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# make temp directory for placement of indices and copy reference file there
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tmp_dir = tempfile.gettempdir()
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try:
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os.system('cp %s %s' % (options.ref, tmp_dir))
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except Exception, erf:
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stop_err('Error creating temp directory for indexing purposes\n' + str(erf))
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if options.fileType == 'solid':
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indexing_cmds = '-c -a %s' % options.indexingAlg
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else:
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indexing_cmds = '-a %s' % options.indexingAlg
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options.ref = os.path.join(tmp_dir,os.path.split(options.ref)[1])
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cmd1 = 'bwa index %s %s 2> /dev/null' % (indexing_cmds, options.ref)
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try:
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os.system(cmd1)
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except Exception, erf:
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stop_err('Error indexing reference sequence\n' + str(erf))
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# set up aligning and generate aligning command options
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if options.params == 'pre_set':
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if options.fileType == 'solid':
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aligning_cmds = '-c'
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else:
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aligning_cmds = ''
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gen_alignment_cmds = ''
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else:
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aligning_cmds = '-n %s -o %s -e %s -d %s -i %s %s -k %s -t %s -M %s -O %s -E %s %s %s %s' % \
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((options.fracMissingAligns, options.maxEditDist)[options.maxEditDist != '0'],
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options.maxGapOpens, options.maxGapExtens, options.disallowLongDel,
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options.disallowIndel, ('',' -l %s'%options.seed)[options.seed!=-1],
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options.maxEditDistSeed, options.numThreads, options.mismatchPenalty,
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options.gapOpenPenalty, options.gapExtensPenalty, ('',' -c')[options.colorSpaceRev=='true'],
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('',' -R')[options.suboptAlign=='true'], ('',' -N')[options.noIterSearch=='true'])
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if options.genAlignType == 'single':
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gen_alignment_cmds = '-n %s' % options.outputTopN
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elif options.genAlignType == 'paired':
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gen_alignment_cmds = '-a %s -o %s' % (options.maxInsertSize, options.maxOccurPairing)
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# set up output file
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file(options.output,'w').write('QNAME\tFLAG\tRNAME\tPOS\tMAPQ\tCIGAR\tMRNM\tMPOS\tISIZE\tSEQ\tQUAL\tOPT\n')
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tmp_align_out = tempfile.NamedTemporaryFile()
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# prepare actual aligning and generate aligning commands
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cmd2 = 'bwa aln %s %s %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.fastq, tmp_align_out.name)
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cmd2b = ''
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if options.genAlignType == 'paired':
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tmp_align_out2 = tempfile.NamedTemporaryFile()
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cmd2b = 'bwa aln %s %s %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.rfastq, tmp_align_out2.name)
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cmd3 = 'bwa sampe %s %s %s %s %s %s >> %s 2> /dev/null' % (gen_alignment_cmds, options.ref, tmp_align_out.name, tmp_align_out2.name, options.fastq, options.rfastq, options.output)
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else:
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cmd3 = 'bwa samse %s %s %s %s >> %s 2> /dev/null' % (gen_alignment_cmds, options.ref, tmp_align_out.name, options.fastq, options.output)
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# align
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try:
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os.system(cmd2)
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except Exception, erf:
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stop_err("Error aligning sequence\n" + str(erf))
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# and again if paired data
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try:
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if cmd2b:
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os.system(cmd2b)
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except Exception, erf:
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stop_err("Error aligning second sequence\n" + str(erf))
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# generate align
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try:
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os.system(cmd3)
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except Exception, erf:
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stop_err("Error sequence aligning sequence\n" + str(erf))
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if __name__=="__main__": __main__()
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@@ -0,0 +1,409 @@
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<tool id="bwa_wrapper" name="BWA" version="1.0.0">
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<description> fast mapping of reads against reference sequence</description>
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<command interpreter="python">
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bwa_wrapper.py
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#if $solidOrSolexa.solidRefGenomeSource.refGenomeSource == "history":
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--ref=$solidOrSolexa.solidRefGenomeSource.ownFile
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--indexingAlg=$solidOrSolexa.solidRefGenomeSource.algorithm
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#else:
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--ref=$solidOrSolexa.solidRefGenomeSource.indices.value
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--indexingAlg="None"
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#end if
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--fastq=$paired.input1
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#if $paired.sPaired == "paired":
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--rfastq=$paired.input2
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#else:
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--rfastq="None"
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#end if
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--output=$output
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--genAlignType=$paired.sPaired
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--params=$params.source_select
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--fileType=$solidOrSolexa.solidSolexa
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--fileSource=$solidOrSolexa.solidRefGenomeSource.refGenomeSource
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#if $params.source_select == "pre_set":
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--maxEditDist="None"
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--fracMissingAligns="None"
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--maxGapOpens="None"
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--maxGapExtens="None"
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--disallowLongDel="None"
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--disallowIndel="None"
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--seed="None"
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--maxEditDistSeed="None"
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--numThreads="None"
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--mismatchPenalty="None"
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--gapOpenPenalty="None"
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--gapExtensPenalty="None"
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--colorSpaceRev="None"
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--suboptAlign="None"
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--noIterSearch="None"
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--outputTopN="None"
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--maxInsertSize="None"
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--maxOccurPairing="None"
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#else:
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--maxEditDist=$params.maxEditDist
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--fracMissingAligns=$params.fracMissingAligns
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--maxGapOpens=$params.maxGapOpens
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--maxGapExtens=$params.maxGapExtens
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--disallowLongDel=$params.disallowLongDel
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--disallowIndel=$params.disallowIndel
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--seed=$params.seed
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--maxEditDistSeed=$params.maxEditDistSeed
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--numThreads=$params.numThreads
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--mismatchPenalty=$params.mismatchPenalty
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--gapOpenPenalty=$params.gapOpenPenalty
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--gapExtensPenalty=$params.gapExtensPenalty
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--colorSpaceRev=$params.colorSpaceRev
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--suboptAlign=$params.suboptAlign
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--noIterSearch=$params.noIterSearch
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--outputTopN=$params.outputTopN
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--maxInsertSize=$params.maxInsertSize
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--maxOccurPairing=$params.maxOccurPairing
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#end if
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</command>
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<inputs>
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<conditional name="solidOrSolexa">
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<param name="solidSolexa" type="select" label="Select SOLiD or Solexa format for the original dataset">
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<option value="solexa">Solexa</option>
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<option value="solid">SOLiD</option>
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</param>
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<when value="solid">
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<conditional name="solidRefGenomeSource">
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<param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
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<option value="indexed">Use a built-in index</option>
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<option value="history">Use one from the history</option>
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</param>
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<when value="history">
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<param name="ownFile" type="data" label="Select a reference genome" />
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<param name="algorithm" type="select" label="Select an indexing algorithm" help="IS works on databses 2GB or less, and is linear-time. BWT-SW works on database 10MB and larger, and trades speed for memory.">
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<option value="is">IS</option>
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<option value="bwtsw">BWT-SW</option>
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</param>
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</when>
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<when value="indexed">
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<param name="indices" type="select" label="Select a reference genome">
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<options from_file="sequence_index_color.loc">
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<column name="value" index="1" />
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<column name="name" index="0" />
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<filter type="sort_by" column="0" />
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</options>
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</param>
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</when>
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</conditional>
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</when>
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<when value="solexa">
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<conditional name="solidRefGenomeSource">
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<param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
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<option value="indexed">Use a built-in index</option>
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<option value="history">Use one from the history</option>
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</param>
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<when value="history">
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<param name="ownFile" type="data" label="Select a reference genome" />
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<param name="algorithm" type="select" label="Select an indexing algorithm" help="IS works on databses 2GB or less, and is linear-time. BWT-SW works on database 10MB and larger, and trades speed for memory.">
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<option value="is">IS</option>
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<option value="bwtsw">BWT-SW</option>
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</param>
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</when>
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<when value="indexed">
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<param name="indices" type="select" label="Select a reference genome">
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<options from_file="sequence_index_base.loc">
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<column name="value" index="1" />
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<column name="name" index="0" />
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<filter type="sort_by" column="0" />
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</options>
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</param>
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</when>
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</conditional>
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</when>
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</conditional>
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<conditional name="paired">
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<param name="sPaired" type="select" label="Is this library mate-paired?">
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<option value="single">Single-end</option>
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<option value="paired">Paired-end</option>
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</param>
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<when value="single">
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<param name="input1" type="data" label="FASTQ file" />
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</when>
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<when value="paired">
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<param name="input1" type="data" label="Forward FASTQ file" />
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<param name="input2" type="data" label="Reverse FASTQ file" />
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</when>
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</conditional>
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<conditional name="params">
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<param name="source_select" type="select" label="BWA settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List">
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<option value="pre_set">Commonly used</option>
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<option value="full">Full Parameter List</option>
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</param>
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<when value="pre_set" />
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<when value="full">
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<param name="maxEditDist" type="integer" value="0" label="Maximum edit distance" help="Enter this value OR a fraction of missing alignments, not both" />
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<param name="fracMissingAligns" type="float" value="0.04" label="Fraction of missing alignments given 2% uniform base error rate" help="Enter this value OR maximum edit distance, not both" />
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<param name="maxGapOpens" type="integer" value="1" label="Maximum number of gap opens" />
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<param name="maxGapExtens" type="integer" value="-1" label="Maximum number of gap extensions" help="-1 for k-difference mode (disallowing long gaps)" />
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<param name="disallowLongDel" type="integer" value="16" label="Disallow long deletion within [value] towards the 3'-end" />
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<param name="disallowIndel" type="integer" value="5" label="Disallow insertion/deletion within [value] bp towards the end" />
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<param name="seed" type="integer" value="-1" label="Number of first subsequences to take as seed" help="Enter -1 for infinity" />
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<param name="maxEditDistSeed" type="integer" value="2" label="Maximum edit distance in the seed" />
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<param name="numThreads" type="integer" value="1" label="Number of threads, in multi-threading mode" />
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<param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty" help="BWA will not search for suboptimal hits with a score lower than [value]" />
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<param name="gapOpenPenalty" type="integer" value="1" label="Gap open penalty" />
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<param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty" />
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<param name="colorSpaceRev" type="select" label="Reverse query but don't compement it" help="Reverse query for all alignment in color space">
|
||||
<option value="false">Don't reverse query</option>
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<option value="true">Reverse query</option>
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</param>
|
||||
<param name="suboptAlign" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Proceed with suboptimal alignments even if the top hit is a repeat" help="By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" />
|
||||
<param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default." />
|
||||
<param name="outputTopN" type="integer" value="-1" label="Output top [value] hits" help="For single-end reads only. Enter -1 to disable outputting multiple hits" />
|
||||
<param name="maxInsertSize" type="integer" value="500" label="Maximum insert size for a read pair to be considered as being mapped properly" help="For paired-end reads only. Only used when there are not enough good alignment to infer the distribution of insert sizes" />
|
||||
<param name="maxOccurPairing" type="integer" value="100000" label="Maximum occurrences of a read for pairing" help="For paired-end reads only. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing" />
|
||||
</when>
|
||||
</conditional>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data format="tabular" name="output" />
|
||||
</outputs>
|
||||
<!-- Tests all fail because of problem with nested conditionals in test framework
|
||||
<tests>
|
||||
<test>
|
||||
<param name="solidSolexa" value="solexa" />
|
||||
<param name="refGenomeSource" value="indexed" />
|
||||
<param name="indices" value="phiX" />
|
||||
<param name="sPaired" value="single" />
|
||||
<param name="input1" value="bwa_phiX_sanger.fastq" />
|
||||
<param name="source_select" value="pre_set" />
|
||||
<output name="output" file="bwa_wrapper_out0.tabular" />
|
||||
</test>
|
||||
<test>
|
||||
<param name="solidSolexa" value="solid" />
|
||||
<param name="refGenomeSource" value="history" />
|
||||
<param name="ownFile" value="phiX.fa" />
|
||||
<param name="algorithm" value="is" />
|
||||
<param name="sPaired" value="single" />
|
||||
<param name="input1" value="bwa_phiX_sanger.fastq" />
|
||||
<param name="source_select" value="pre_set" />
|
||||
<output name="output" file="bwa_wrapper_out0b.tabular" />
|
||||
</test>
|
||||
<test>
|
||||
<param name="solidSolexa" value="solid" />
|
||||
<param name="refGenomeSource" value="indexed" />
|
||||
<param name="indices" value="phiX" />
|
||||
<param name="sPaired" value="single" />
|
||||
<param name="input1" value="bwa_solid.fastq" />
|
||||
<param name="source_select" value="full" />
|
||||
<param name="maxEditDist" value="0" />
|
||||
<param name="fracMissingAligns" value="0.04" />
|
||||
<param name="maxGapOpens" value="1" />
|
||||
<param name="maxGapExtens" value="-1" />
|
||||
<param name="disallowLongDel" value="16" />
|
||||
<param name="disallowIndel" value="5" />
|
||||
<param name="seed" value="-1" />
|
||||
<param name="maxEditDistSeed" value="2" />
|
||||
<param name="numThreads" value="1" />
|
||||
<param name="mismatchPenalty" value="3" />
|
||||
<param name="gapOpenPenalty" value="1" />
|
||||
<param name="gapExtensPenalty" value="4" />
|
||||
<param name="colorSpaceRev" value="true" />
|
||||
<param name="suboptAlign" value="true" />
|
||||
<param name="noIterSearch" value="true" />
|
||||
<param name="outputTopN" value="-1" />
|
||||
<param name="maxInsertSize" value="500" />
|
||||
<param name="maxOccurPairing" value="100000" />
|
||||
<output name="output" file="bwa_wrapper_out1.tabular" />
|
||||
</test>
|
||||
<test>
|
||||
<param name="solidSolexa" value="solid" />
|
||||
<param name="refGenomeSource" value="indexed" />
|
||||
<param name="indices" value="phiX" />
|
||||
<param name="sPaired" value="paired" />
|
||||
<param name="input1" value="bwa_solid_f.fastq" />
|
||||
<param name="input2" value="bwa_solid_r.fastq" />
|
||||
<param name="source_select" value="full" />
|
||||
<param name="maxEditDist" value="0" />
|
||||
<param name="fracMissingAligns" value="0.04" />
|
||||
<param name="maxGapOpens" value="1" />
|
||||
<param name="maxGapExtens" value="-1" />
|
||||
<param name="disallowLongDel" value="16" />
|
||||
<param name="disallowIndel" value="5" />
|
||||
<param name="seed" value="-1" />
|
||||
<param name="maxEditDistSeed" value="2" />
|
||||
<param name="numThreads" value="1" />
|
||||
<param name="mismatchPenalty" value="3" />
|
||||
<param name="gapOpenPenalty" value="1" />
|
||||
<param name="gapExtensPenalty" value="4" />
|
||||
<param name="colorSpaceRev" value="true" />
|
||||
<param name="suboptAlign" value="true" />
|
||||
<param name="noIterSearch" value="true" />
|
||||
<param name="outputTopN" value="-1" />
|
||||
<param name="maxInsertSize" value="500" />
|
||||
<param name="maxOccurPairing" value="100000" />
|
||||
<output name="output" file="bwa_wrapper_out2.tabular" />
|
||||
</test>
|
||||
<test>
|
||||
<param name="solidSolexa" value="solexa" />
|
||||
<param name="refGenomeSource" value="indexed" />
|
||||
<param name="indices" value="phiX" />
|
||||
<param name="sPaired" value="single" />
|
||||
<param name="input1" value="bwa_phiX_sanger.fastq" />
|
||||
<param name="source_select" value="full" />
|
||||
<param name="maxEditDist" value="0" />
|
||||
<param name="fracMissingAligns" value="0.04" />
|
||||
<param name="maxGapOpens" value="1" />
|
||||
<param name="maxGapExtens" value="-1" />
|
||||
<param name="disallowLongDel" value="16" />
|
||||
<param name="disallowIndel" value="5" />
|
||||
<param name="seed" value="-1" />
|
||||
<param name="maxEditDistSeed" value="2" />
|
||||
<param name="numThreads" value="1" />
|
||||
<param name="mismatchPenalty" value="3" />
|
||||
<param name="gapOpenPenalty" value="1" />
|
||||
<param name="gapExtensPenalty" value="4" />
|
||||
<param name="colorSpaceRev" value="false" />
|
||||
<param name="suboptAlign" value="true" />
|
||||
<param name="noIterSearch" value="true" />
|
||||
<param name="outputTopN" value="-1" />
|
||||
<param name="maxInsertSize" value="500" />
|
||||
<param name="maxOccurPairing" value="100000" />
|
||||
<output name="output" file="bwa_wrapper_out3.tabular" />
|
||||
</test>
|
||||
<test>
|
||||
<param name="solidSolexa" value="solexa" />
|
||||
<param name="refGenomeSource" value="indexed" />
|
||||
<param name="indices" value="phiX" />
|
||||
<param name="sPaired" value="paired" />
|
||||
<param name="input1" value="bwa_phiX_sanger_f.fastq" />
|
||||
<param name="input2" value="bwa_phiX_sanger_r.fastq" />
|
||||
<param name="source_select" value="full" />
|
||||
<param name="maxEditDist" value="0" />
|
||||
<param name="fracMissingAligns" value="0.04" />
|
||||
<param name="maxGapOpens" value="1" />
|
||||
<param name="maxGapExtens" value="-1" />
|
||||
<param name="disallowLongDel" value="16" />
|
||||
<param name="disallowIndel" value="5" />
|
||||
<param name="seed" value="-1" />
|
||||
<param name="maxEditDistSeed" value="2" />
|
||||
<param name="numThreads" value="1" />
|
||||
<param name="mismatchPenalty" value="3" />
|
||||
<param name="gapOpenPenalty" value="1" />
|
||||
<param name="gapExtensPenalty" value="4" />
|
||||
<param name="colorSpaceRev" value="false" />
|
||||
<param name="suboptAlign" value="true" />
|
||||
<param name="noIterSearch" value="true" />
|
||||
<param name="outputTopN" value="-1" />
|
||||
<param name="maxInsertSize" value="500" />
|
||||
<param name="maxOccurPairing" value="100000" />
|
||||
<output name="output" file="bwa_wrapper_out4.tabular" />
|
||||
</test>
|
||||
</tests>
|
||||
-->
|
||||
<help>
|
||||
|
||||
**What it does**
|
||||
|
||||
**BWA** is a high performance sequence aligner that succeeds MAQ. It is based on BWT-SW but uses a completely different algorithm, and it is aimed toward short read alignments. It is fast--it can map the human genome in only 15-25 minutes. Heng Li of the Sanger Institute wrote the majority of the code, with contributions by Chi-Kwong Wong at the University of Hong Kong, Nong Ge at Sun Yat-Sen University, and Yuta Mori.
|
||||
|
||||
------
|
||||
|
||||
**Input formats**
|
||||
|
||||
BWA accepts files in FASTQ format.
|
||||
|
||||
------
|
||||
|
||||
**Outputs**
|
||||
|
||||
The output is in SAM format, and has the following columns::
|
||||
|
||||
1 QNAME - Query (pair) NAME
|
||||
2 FLAG - bitwise FLAG
|
||||
3 RNAME - Reference sequence NAME
|
||||
4 POS - 1-based leftmost POSition/coordinate of clipped sequence
|
||||
5 MAPQ - MAPping Quality (Phred-scaled)
|
||||
6 CIGAR - extended CIGAR string
|
||||
7 MRNM - Mate Reference sequence NaMe ('=' if same as RNAME)
|
||||
8 MPOS - 1-based Mate POSition
|
||||
9 ISIZE - Inferred insert SIZE
|
||||
10 SEQ - query SEQuence on the same strand as the reference
|
||||
11 QUAL - query QUALity (ASCII-33 gives the Phred base quality)
|
||||
12 OPT - variable OPTional fields in the format TAG:VTYPE:VALU
|
||||
|
||||
The flags are as follows::
|
||||
|
||||
Flag - Description
|
||||
0x0001 - the read is paired in sequencing
|
||||
0x0002 - the read is mapped in a proper pair
|
||||
0x0004 - the query sequence itself is unmapped
|
||||
0x0008 - the mate is unmapped
|
||||
0x0010 - strand of the query (1 for reverse)
|
||||
0x0020 - strand of the mate
|
||||
0x0040 - the read is the first read in a pair
|
||||
0x0080 - the read is the second read in a pair
|
||||
0x0100 - the alignment is not primary
|
||||
|
||||
It looks like this (scroll sideways to see the entire example)::
|
||||
|
||||
QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
|
||||
HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
|
||||
HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
|
||||
|
||||
-------
|
||||
|
||||
**BWA Settings**
|
||||
|
||||
All of the options have a default value. You can change any of them. All of the options in BWA have been implemented here.
|
||||
|
||||
------
|
||||
|
||||
**BWA parameter list**
|
||||
|
||||
This is an exhaustive list of BWA options:
|
||||
|
||||
For **aln**::
|
||||
|
||||
-n NUM Maximum edit distance if the value is INT, or the fraction of missing
|
||||
alignments given 2% uniform base error rate if FLOAT. In the latter
|
||||
case, the maximum edit distance is automatically chosen for different
|
||||
read lengths. [0.04]
|
||||
-o INT Maximum number of gap opens [1]
|
||||
-e INT Maximum number of gap extensions, -1 for k-difference mode
|
||||
(disallowing long gaps) [-1]
|
||||
-d INT Disallow a long deletion within INT bp towards the 3'-end [16]
|
||||
-i INT Disallow an indel within INT bp towards the ends [5]
|
||||
-l INT Take the first INT subsequence as seed. If INT is larger than the
|
||||
query sequence, seeding will be disabled. For long reads, this option
|
||||
is typically ranged from 25 to 35 for '-k 2'. [inf]
|
||||
-k INT Maximum edit distance in the seed [2]
|
||||
-t INT Number of threads (multi-threading mode) [1]
|
||||
-M INT Mismatch penalty. BWA will not search for suboptimal hits with a score
|
||||
lower than (bestScore-misMsc). [3]
|
||||
-O INT Gap open penalty [11]
|
||||
-E INT Gap extension penalty [4]
|
||||
-c Reverse query but not complement it, which is required for alignment
|
||||
in the color space.
|
||||
-R Proceed with suboptimal alignments even if the top hit is a repeat. By
|
||||
default, BWA only searches for suboptimal alignments if the top hit is
|
||||
unique. Using this option has no effect on accuracy for single-end
|
||||
reads. It is mainly designed for improving the alignment accuracy of
|
||||
paired-end reads. However, the pairing procedure will be slowed down,
|
||||
especially for very short reads (~32bp).
|
||||
-N Disable iterative search. All hits with no more than maxDiff
|
||||
differences will be found. This mode is much slower than the default.
|
||||
|
||||
For **samse**::
|
||||
|
||||
-n INT Output up to INT top hits. Value -1 to disable outputting multiple
|
||||
hits. [-1]
|
||||
|
||||
For **sampe**::
|
||||
|
||||
-a INT Maximum insert size for a read pair to be considered as being mapped
|
||||
properly. Since 0.4.5, this option is only used when there are not
|
||||
enough good alignment to infer the distribution of insert sizes. [500]
|
||||
-o INT Maximum occurrences of a read for pairing. A read with more
|
||||
occurrences will be treated as a single-end read. Reducing this
|
||||
parameter helps faster pairing. [100000]
|
||||
|
||||
|
||||
</help>
|
||||
</tool>
|
||||
|
||||
|
||||
Reference in New Issue
Block a user