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comparison bwa_wrapper.xml @ 0:ffa8aaa14f7c draft

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author devteam
date Fri, 28 Sep 2012 13:53:48 -0400
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1 <tool id="bwa_wrapper" name="Map with BWA for Illumina" version="1.2.3">
2 <requirements>
3 <requirement type="package" version="0.5.9">bwa</requirement>
4 </requirements>
5 <description></description>
6 <parallelism method="basic"></parallelism>
7 <command interpreter="python">
8 bwa_wrapper.py
9 --threads="4"
10
11 #if $input1.ext == "fastqillumina":
12 --illumina1.3
13 #end if
14
15 ## reference source
16 --fileSource=$genomeSource.refGenomeSource
17 #if $genomeSource.refGenomeSource == "history":
18 ##build index on the fly
19 --ref="${genomeSource.ownFile}"
20 --dbkey=$dbkey
21 #else:
22 ##use precomputed indexes
23 --ref="${genomeSource.indices.fields.path}"
24 --do_not_build_index
25 #end if
26
27 ## input file(s)
28 --input1=$paired.input1
29 #if $paired.sPaired == "paired":
30 --input2=$paired.input2
31 #end if
32
33 ## output file
34 --output=$output
35
36 ## run parameters
37 --genAlignType=$paired.sPaired
38 --params=$params.source_select
39 #if $params.source_select != "pre_set":
40 --maxEditDist=$params.maxEditDist
41 --fracMissingAligns=$params.fracMissingAligns
42 --maxGapOpens=$params.maxGapOpens
43 --maxGapExtens=$params.maxGapExtens
44 --disallowLongDel=$params.disallowLongDel
45 --disallowIndel=$params.disallowIndel
46 --seed=$params.seed
47 --maxEditDistSeed=$params.maxEditDistSeed
48 --mismatchPenalty=$params.mismatchPenalty
49 --gapOpenPenalty=$params.gapOpenPenalty
50 --gapExtensPenalty=$params.gapExtensPenalty
51 --suboptAlign="${params.suboptAlign}"
52 --noIterSearch=$params.noIterSearch
53 --outputTopN=$params.outputTopN
54 --outputTopNDisc=$params.outputTopNDisc
55 --maxInsertSize=$params.maxInsertSize
56 --maxOccurPairing=$params.maxOccurPairing
57 #if $params.readGroup.specReadGroup == "yes"
58 --rgid="$params.readGroup.rgid"
59 --rgcn="$params.readGroup.rgcn"
60 --rgds="$params.readGroup.rgds"
61 --rgdt="$params.readGroup.rgdt"
62 --rgfo="$params.readGroup.rgfo"
63 --rgks="$params.readGroup.rgks"
64 --rglb="$params.readGroup.rglb"
65 --rgpg="$params.readGroup.rgpg"
66 --rgpi="$params.readGroup.rgpi"
67 --rgpl="$params.readGroup.rgpl"
68 --rgpu="$params.readGroup.rgpu"
69 --rgsm="$params.readGroup.rgsm"
70 #end if
71 #end if
72
73 ## suppress output SAM header
74 --suppressHeader=$suppressHeader
75 </command>
76 <inputs>
77 <conditional name="genomeSource">
78 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
79 <option value="indexed">Use a built-in index</option>
80 <option value="history">Use one from the history</option>
81 </param>
82 <when value="indexed">
83 <param name="indices" type="select" label="Select a reference genome">
84 <options from_data_table="bwa_indexes">
85 <filter type="sort_by" column="2" />
86 <validator type="no_options" message="No indexes are available" />
87 </options>
88 </param>
89 </when>
90 <when value="history">
91 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
92 </when>
93 </conditional>
94 <conditional name="paired">
95 <param name="sPaired" type="select" label="Is this library mate-paired?">
96 <option value="single">Single-end</option>
97 <option value="paired">Paired-end</option>
98 </param>
99 <when value="single">
100 <param name="input1" type="data" format="fastqsanger,fastqillumina" label="FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
101 </when>
102 <when value="paired">
103 <param name="input1" type="data" format="fastqsanger,fastqillumina" label="Forward FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
104 <param name="input2" type="data" format="fastqsanger,fastqillumina" label="Reverse FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
105 </when>
106 </conditional>
107 <conditional name="params">
108 <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 Parameter List">
109 <option value="pre_set">Commonly Used</option>
110 <option value="full">Full Parameter List</option>
111 </param>
112 <when value="pre_set" />
113 <when value="full">
114 <param name="maxEditDist" type="integer" value="0" label="Maximum edit distance (aln -n)" help="Enter this value OR a fraction of missing alignments, not both" />
115 <param name="fracMissingAligns" type="float" value="0.04" label="Fraction of missing alignments given 2% uniform base error rate (aln -n)" help="Enter this value OR maximum edit distance, not both" />
116 <param name="maxGapOpens" type="integer" value="1" label="Maximum number of gap opens (aln -o)" />
117 <param name="maxGapExtens" type="integer" value="-1" label="Maximum number of gap extensions (aln -e)" help="-1 for k-difference mode (disallowing long gaps)" />
118 <param name="disallowLongDel" type="integer" value="16" label="Disallow long deletion within [value] bp towards the 3'-end (aln -d)" />
119 <param name="disallowIndel" type="integer" value="5" label="Disallow insertion/deletion within [value] bp towards the end (aln -i)" />
120 <param name="seed" type="integer" value="-1" label="Number of first subsequences to take as seed (aln -l)" help="Enter -1 for infinity" />
121 <param name="maxEditDistSeed" type="integer" value="2" label="Maximum edit distance in the seed (aln -k)" />
122 <param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty (aln -M)" help="BWA will not search for suboptimal hits with a score lower than [value]" />
123 <param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (aln -O)" />
124 <param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (aln -E)" />
125 <param name="suboptAlign" type="integer" optional="True" label="Proceed with suboptimal alignments if there are no more than INT equally best hits. (aln -R)" help="For paired-end reads only. 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)" />
126 <param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search (aln -N)" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default" />
127 <param name="outputTopN" type="integer" value="3" label="Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n)" help="If a read has more than INT hits, the XA tag will not be written" />
128 <param name="outputTopNDisc" type="integer" value="10" label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N)" help="For paired-end reads only. If a read has more than INT hits, the XA tag will not be written" />
129 <param name="maxInsertSize" type="integer" value="500" label="Maximum insert size for a read pair to be considered as being mapped properly (sampe -a)" help="For paired-end reads only. Only used when there are not enough good alignments to infer the distribution of insert sizes" />
130 <param name="maxOccurPairing" type="integer" value="100000" label="Maximum occurrences of a read for pairing (sampe -o)" 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" />
131 <conditional name="readGroup">
132 <param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)">
133 <option value="yes">Yes</option>
134 <option value="no" selected="True">No</option>
135 </param>
136 <when value="yes">
137 <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG
138 tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group
139 IDs may be modified when merging SAM files in order to handle collisions." />
140 <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read (CN)" help="Optional" />
141 <param name="rgds" type="text" size="25" label="Description (DS)" help="Optional" />
142 <param name="rgdt" type="text" size="25" label="Date that run was produced (DT)" help="Optional. ISO8601 format date or date/time, like YYYY-MM-DD" />
143 <param name="rgfo" type="text" size="25" label="Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each
144 flow of each read." help="Optional. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by
145 various other characters. Format : /\*|[ACMGRSVTWYHKDBN]+/" />
146 <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" help="Optional" />
147 <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" />
148 <param name="rgpg" type="text" size="25" label="Programs used for processing the read group (PG)" help="Optional" />
149 <param name="rgpi" type="text" size="25" label="Predicted median insert size (PI)" help="Optional" />
150 <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA,
151 SOLID, HELICOS, IONTORRENT and PACBIO" />
152 <param name="rgpu" type="text" size="25" label="Platform unit (PU)" help="Optional. Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" />
153 <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" />
154 </when>
155 <when value="no" />
156 </conditional>
157 </when>
158 </conditional>
159 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" />
160 </inputs>
161 <outputs>
162 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
163 <actions>
164 <conditional name="genomeSource.refGenomeSource">
165 <when value="indexed">
166 <action type="metadata" name="dbkey">
167 <option type="from_data_table" name="bwa_indexes" column="1">
168 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
169 <filter type="param_value" ref="genomeSource.indices" column="0"/>
170 </option>
171 </action>
172 </when>
173 <when value="history">
174 <action type="metadata" name="dbkey">
175 <option type="from_param" name="genomeSource.ownFile" param_attribute="dbkey" />
176 </action>
177 </when>
178 </conditional>
179 </actions>
180 </data>
181 </outputs>
182 <tests>
183 <test>
184 <!--
185 BWA commands:
186 bwa aln -t 4 phiX.fasta test-data/bwa_wrapper_in1.fastqsanger > bwa_wrapper_out1.sai
187 bwa samse phiX.fasta bwa_wrapper_out1.sai test-data/bwa_wrapper_in1.fastqsanger > bwa_wrapper_out1.sam
188 phiX.fasta is the prefix for the reference files (phiX.fasta.amb, phiX.fasta.ann, phiX.fasta.bwt, ...)
189 remove the comment lines (beginning with '@') from the resulting sam file
190 plain old sort doesn't handle underscores like python:
191 python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out1.u.sam bwa_wrapper_out1.sam
192 -->
193 <param name="refGenomeSource" value="indexed" />
194 <param name="indices" value="phiX" />
195 <param name="sPaired" value="single" />
196 <param name="input1" value="bwa_wrapper_in1.fastqsanger" ftype="fastqsanger" />
197 <param name="source_select" value="pre_set" />
198 <param name="suppressHeader" value="true" />
199 <output name="output" file="bwa_wrapper_out1.sam" ftype="sam" sort="True" />
200 </test>
201 <test>
202 <!--
203 BWA commands:
204 cp test-data/phiX.fasta phiX.fasta
205 bwa index -a is phiX.fasta
206 bwa aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -k 2 -t 4 -M 3 -O 11 -E 4 -R -N phiX.fasta test-data/bwa_wrapper_in1.fastqsanger > bwa_wrapper_out2.sai
207 bwa samse -n 3 phiX.fasta bwa_wrapper_out2.sai test-data/bwa_wrapper_in1.fastqsanger > bwa_wrapper_out2.u.sam
208 phiX.fasta is the prefix for the reference files (phiX.fasta.amb, phiX.fasta.ann, phiX.fasta.bwt, ...)
209 remove the comment lines (beginning with '@') from the resulting sam file
210 plain old sort doesn't handle underscores like python:
211 python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out2.u.sam bwa_wrapper_out2.sam
212 -->
213 <param name="refGenomeSource" value="history" />
214 <param name="ownFile" value="phiX.fasta" />
215 <param name="sPaired" value="single" />
216 <param name="input1" value="bwa_wrapper_in1.fastqsanger" ftype="fastqsanger" />
217 <param name="source_select" value="full" />
218 <param name="maxEditDist" value="0" />
219 <param name="fracMissingAligns" value="0.04" />
220 <param name="maxGapOpens" value="1" />
221 <param name="maxGapExtens" value="-1" />
222 <param name="disallowLongDel" value="16" />
223 <param name="disallowIndel" value="5" />
224 <param name="seed" value="-1" />
225 <param name="maxEditDistSeed" value="2" />
226 <param name="mismatchPenalty" value="3" />
227 <param name="gapOpenPenalty" value="11" />
228 <param name="gapExtensPenalty" value="4" />
229 <param name="suboptAlign" value="" />
230 <param name="noIterSearch" value="true" />
231 <param name="outputTopN" value="3" />
232 <param name="outputTopNDisc" value="10" />
233 <param name="maxInsertSize" value="500" />
234 <param name="maxOccurPairing" value="100000" />
235 <param name="specReadGroup" value="no" />
236 <param name="suppressHeader" value="true" />
237 <output name="output" file="bwa_wrapper_out2.sam" ftype="sam" sort="True" />
238 </test>
239 <test>
240 <!--
241 BWA commands:
242 bwa aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -k 2 -t 4 -M 3 -O 11 -E 4 -R -N phiX.fasta test-data/bwa_wrapper_in2.fastqsanger > bwa_wrapper_out3a.sai
243 bwa aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -k 2 -t 4 -M 3 -O 11 -E 4 -R -N phiX.fasta test-data/bwa_wrapper_in3.fastqsanger > bwa_wrapper_out3b.sai
244 bwa sampe -a 500 -o 100000 -n 3 -N 10 -r "@RG\tID:abcdefg\tDS:descrip\tDT:2010-11-01\tLB:lib-mom-A\tPI:400\tPL:ILLUMINA\tSM:mom" phiX.fasta bwa_wrapper_out3a.sai bwa_wrapper_out3b.sai test-data/bwa_wrapper_in2.fastqsanger test-data/bwa_wrapper_in3.fastqsanger > bwa_wrapper_out3.u.sam
245 phiX.fasta is the prefix for the reference
246 plain old sort doesn't handle underscores like python:
247 python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out3.u.sam bwa_wrapper_out3.sam
248 -->
249 <param name="refGenomeSource" value="indexed" />
250 <param name="indices" value="phiX" />
251 <param name="sPaired" value="paired" />
252 <param name="input1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
253 <param name="input2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" />
254 <param name="source_select" value="full" />
255 <param name="maxEditDist" value="0" />
256 <param name="fracMissingAligns" value="0.04" />
257 <param name="maxGapOpens" value="1" />
258 <param name="maxGapExtens" value="-1" />
259 <param name="disallowLongDel" value="16" />
260 <param name="disallowIndel" value="5" />
261 <param name="seed" value="-1" />
262 <param name="maxEditDistSeed" value="2" />
263 <param name="mismatchPenalty" value="3" />
264 <param name="gapOpenPenalty" value="11" />
265 <param name="gapExtensPenalty" value="4" />
266 <param name="suboptAlign" value="" />
267 <param name="noIterSearch" value="true" />
268 <param name="outputTopN" value="3" />
269 <param name="outputTopNDisc" value="10" />
270 <param name="maxInsertSize" value="500" />
271 <param name="maxOccurPairing" value="100000" />
272 <param name="specReadGroup" value="yes" />
273 <param name="rgid" value="abcdefg" />
274 <param name="rgcn" value="" />
275 <param name="rgds" value="descrip" />
276 <param name="rgdt" value="2010-11-01" />
277 <param name="rgfo" value="" />
278 <param name="rgks" value="" />
279 <param name="rglb" value="lib-mom-A" />
280 <param name="rgpg" value="" />
281 <param name="rgpi" value="400" />
282 <param name="rgpl" value="ILLUMINA" />
283 <param name="rgpu" value="" />
284 <param name="rgsm" value="mom" />
285 <param name="suppressHeader" value="false" />
286 <output name="output" file="bwa_wrapper_out3.sam" ftype="sam" sort="True" lines_diff="2" />
287 </test>
288 <test>
289 <!--
290 BWA commands:
291 cp test-data/phiX.fasta phiX.fasta
292 bwa index -a is phiX.fasta
293 bwa aln -t 4 phiX.fasta test-data/bwa_wrapper_in2.fastqsanger > bwa_wrapper_out8a.sai
294 bwa aln -t 4 phiX.fasta test-data/bwa_wrapper_in3.fastqsanger > bwa_wrapper_out8b.sai
295 bwa sampe -a 500 -o 100000 phiX.fasta bwa_wrapper_out8a.sai bwa_wrapper_out8b.sai test-data/bwa_wrapper_in2.fastqsanger test-data/bwa_wrapper_in3.fastqsanger > bwa_wrapper_out8.u.sam
296 phiX.fa is the prefix for the reference
297 remove the comment lines (beginning with '@') from the resulting sam file
298 python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out8.u.sam bwa_wrapper_out8.sam
299 -->
300 <param name="refGenomeSource" value="history" />
301 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
302 <param name="ownFile" value="phiX.fasta" />
303 <param name="sPaired" value="paired" />
304 <param name="input1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
305 <param name="input2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" />
306 <param name="source_select" value="preSet" />
307 <param name="suppressHeader" value="true" />
308 <output name="output" file="bwa_wrapper_out8.sam" ftype="sam" sort="True" />
309 </test>
310 </tests>
311 <help>
312
313 **What it does**
314
315 BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (large), such as the human reference genome. It is developed by Heng Li at the Sanger Insitute. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-60.
316
317 ------
318
319 **Know what you are doing**
320
321 .. class:: warningmark
322
323 There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
324
325 .. __: http://bio-bwa.sourceforge.net/
326
327 ------
328
329 **Input formats**
330
331 BWA accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*) or Illumina FASTQ format (galaxy type *fastqillumina*). Use the FASTQ Groomer to prepare your files.
332
333 ------
334
335 **A Note on Built-in Reference Genomes**
336
337 The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
338
339 ------
340
341 **Outputs**
342
343 The output is in SAM format, and has the following columns::
344
345 Column Description
346 -------- --------------------------------------------------------
347 1 QNAME Query (pair) NAME
348 2 FLAG bitwise FLAG
349 3 RNAME Reference sequence NAME
350 4 POS 1-based leftmost POSition/coordinate of clipped sequence
351 5 MAPQ MAPping Quality (Phred-scaled)
352 6 CIGAR extended CIGAR string
353 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
354 8 MPOS 1-based Mate POSition
355 9 ISIZE Inferred insert SIZE
356 10 SEQ query SEQuence on the same strand as the reference
357 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
358 12 OPT variable OPTional fields in the format TAG:VTYPE:VALU
359
360 The flags are as follows::
361
362 Flag Description
363 ------ -------------------------------------
364 0x0001 the read is paired in sequencing
365 0x0002 the read is mapped in a proper pair
366 0x0004 the query sequence itself is unmapped
367 0x0008 the mate is unmapped
368 0x0010 strand of the query (1 for reverse)
369 0x0020 strand of the mate
370 0x0040 the read is the first read in a pair
371 0x0080 the read is the second read in a pair
372 0x0100 the alignment is not primary
373
374 It looks like this (scroll sideways to see the entire example)::
375
376 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
377 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
378 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
379
380 -------
381
382 **BWA settings**
383
384 All of the options have a default value. You can change any of them. All of the options in BWA have been implemented here.
385
386 ------
387
388 **BWA parameter list**
389
390 This is an exhaustive list of BWA options:
391
392 For **aln**::
393
394 -n NUM Maximum edit distance if the value is INT, or the fraction of missing
395 alignments given 2% uniform base error rate if FLOAT. In the latter
396 case, the maximum edit distance is automatically chosen for different
397 read lengths. [0.04]
398 -o INT Maximum number of gap opens [1]
399 -e INT Maximum number of gap extensions, -1 for k-difference mode
400 (disallowing long gaps) [-1]
401 -d INT Disallow a long deletion within INT bp towards the 3'-end [16]
402 -i INT Disallow an indel within INT bp towards the ends [5]
403 -l INT Take the first INT subsequence as seed. If INT is larger than the
404 query sequence, seeding will be disabled. For long reads, this option
405 is typically ranged from 25 to 35 for '-k 2'. [inf]
406 -k INT Maximum edit distance in the seed [2]
407 -t INT Number of threads (multi-threading mode) [1]
408 -M INT Mismatch penalty. BWA will not search for suboptimal hits with a score
409 lower than (bestScore-misMsc). [3]
410 -O INT Gap open penalty [11]
411 -E INT Gap extension penalty [4]
412 -c Reverse query but not complement it, which is required for alignment
413 in the color space.
414 -R Proceed with suboptimal alignments even if the top hit is a repeat. By
415 default, BWA only searches for suboptimal alignments if the top hit is
416 unique. Using this option has no effect on accuracy for single-end
417 reads. It is mainly designed for improving the alignment accuracy of
418 paired-end reads. However, the pairing procedure will be slowed down,
419 especially for very short reads (~32bp).
420 -N Disable iterative search. All hits with no more than maxDiff
421 differences will be found. This mode is much slower than the default.
422
423 For **samse**::
424
425 -n INT Maximum number of alignments to output in the XA tag for reads paired
426 properly. If a read has more than INT hits, the XA tag will not be
427 written. [3]
428 -r STR Specify the read group in a format like '@RG\tID:foo\tSM:bar' [null]
429
430 For **sampe**::
431
432 -a INT Maximum insert size for a read pair to be considered as being mapped
433 properly. Since version 0.4.5, this option is only used when there
434 are not enough good alignment to infer the distribution of insert
435 sizes. [500]
436 -n INT Maximum number of alignments to output in the XA tag for reads paired
437 properly. If a read has more than INT hits, the XA tag will not be
438 written. [3]
439 -N INT Maximum number of alignments to output in the XA tag for disconcordant
440 read pairs (excluding singletons). If a read has more than INT hits,
441 the XA tag will not be written. [10]
442 -o INT Maximum occurrences of a read for pairing. A read with more
443 occurrences will be treated as a single-end read. Reducing this
444 parameter helps faster pairing. [100000]
445 -r STR Specify the read group in a format like '@RG\tID:foo\tSM:bar' [null]
446
447 For specifying the read group in **samse** or **sampe**, use the following::
448
449 @RG Read group. Unordered multiple @RG lines are allowed.
450 ID Read group identifier. Each @RG line must have a unique ID. The value of
451 ID is used in the RG tags of alignment records. Must be unique among all
452 read groups in header section. Read group IDs may be modified when
453 merging SAM files in order to handle collisions.
454 CN Name of sequencing center producing the read.
455 DS Description.
456 DT Date the run was produced (ISO8601 date or date/time).
457 FO Flow order. The array of nucleotide bases that correspond to the
458 nucleotides used for each flow of each read. Multi-base flows are encoded
459 in IUPAC format, and non-nucleotide flows by various other characters.
460 Format : /\*|[ACMGRSVTWYHKDBN]+/
461 KS The array of nucleotide bases that correspond to the key sequence of each read.
462 LB Library.
463 PG Programs used for processing the read group.
464 PI Predicted median insert size.
465 PL Platform/technology used to produce the reads. Valid values : CAPILLARY,
466 LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO.
467 PU Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for
468 SOLiD). Unique identifier.
469 SM Sample. Use pool name where a pool is being sequenced.
470
471 </help>
472 </tool>
473
474