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comparison bwa_wrapper.xml @ 0:8d92246f41bb draft

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author evan
date Thu, 05 Jun 2014 15:15:34 -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="\${GALAXY_SLOTS:-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 #if $params.readGroup.specReadGroup == "from_file"
72 --meta_tsv="$params.readGroup.metadata_tsv"
73 #end if
74 #end if
75
76 ## suppress output SAM header
77 --suppressHeader="${suppressHeader}"
78 </command>
79 <inputs>
80 <conditional name="genomeSource">
81 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
82 <option value="indexed">Use a built-in index</option>
83 <option value="history">Use one from the history</option>
84 </param>
85 <when value="indexed">
86 <param name="indices" type="select" label="Select a reference genome">
87 <options from_data_table="bwa_indexes">
88 <filter type="sort_by" column="2" />
89 <validator type="no_options" message="No indexes are available" />
90 </options>
91 </param>
92 </when>
93 <when value="history">
94 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
95 </when>
96 </conditional>
97 <conditional name="paired">
98 <param name="sPaired" type="select" label="Is this library mate-paired?">
99 <option value="single">Single-end</option>
100 <option value="paired">Paired-end</option>
101 </param>
102 <when value="single">
103 <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)" />
104 </when>
105 <when value="paired">
106 <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)" />
107 <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)" />
108 </when>
109 </conditional>
110 <conditional name="params">
111 <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">
112 <option value="pre_set">Commonly Used</option>
113 <option value="full">Full Parameter List</option>
114 </param>
115 <when value="pre_set" />
116 <when value="full">
117 <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" />
118 <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" />
119 <param name="maxGapOpens" type="integer" value="1" label="Maximum number of gap opens (aln -o)" />
120 <param name="maxGapExtens" type="integer" value="-1" label="Maximum number of gap extensions (aln -e)" help="-1 for k-difference mode (disallowing long gaps)" />
121 <param name="disallowLongDel" type="integer" value="16" label="Disallow long deletion within [value] bp towards the 3'-end (aln -d)" />
122 <param name="disallowIndel" type="integer" value="5" label="Disallow insertion/deletion within [value] bp towards the end (aln -i)" />
123 <param name="seed" type="integer" value="-1" label="Number of first subsequences to take as seed (aln -l)" help="Enter -1 for infinity" />
124 <param name="maxEditDistSeed" type="integer" value="2" label="Maximum edit distance in the seed (aln -k)" />
125 <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]" />
126 <param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (aln -O)" />
127 <param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (aln -E)" />
128 <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)" />
129 <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" />
130 <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" />
131 <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" />
132 <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" />
133 <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" />
134 <conditional name="readGroup">
135 <param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)">
136 <option value="yes">Yes</option>
137 <option value="no" selected="True">No</option>
138 </param>
139 <when value="yes">
140 <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
141 tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group
142 IDs may be modified when merging SAM files in order to handle collisions." />
143 <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read (CN)" help="Optional" />
144 <param name="rgds" type="text" size="25" label="Description (DS)" help="Optional" />
145 <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" />
146 <param name="rgfo" type="text" size="25" label="Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each
147 flow of each read." help="Optional. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by
148 various other characters. Format : /\*|[ACMGRSVTWYHKDBN]+/" />
149 <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" />
150 <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" />
151 <param name="rgpg" type="text" size="25" label="Programs used for processing the read group (PG)" help="Optional" />
152 <param name="rgpi" type="text" size="25" label="Predicted median insert size (PI)" help="Optional" />
153 <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,
154 SOLID, HELICOS, IONTORRENT and PACBIO" />
155 <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)" />
156 <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" />
157 </when>
158 <when value="from_file">
159 <param name="metadata_tsv" type="data" format="txt" label="BMGC tabular metadata" />
160 </when>
161 <when value="no" />
162 </conditional>
163 </when>
164 </conditional>
165 <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" />
166 </inputs>
167 <outputs>
168 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
169 <actions>
170 <conditional name="genomeSource.refGenomeSource">
171 <when value="indexed">
172 <action type="metadata" name="dbkey">
173 <option type="from_data_table" name="bwa_indexes" column="1">
174 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
175 <filter type="param_value" ref="genomeSource.indices" column="0"/>
176 </option>
177 </action>
178 </when>
179 <when value="history">
180 <action type="metadata" name="dbkey">
181 <option type="from_param" name="genomeSource.ownFile" param_attribute="dbkey" />
182 </action>
183 </when>
184 </conditional>
185 </actions>
186 </data>
187 </outputs>
188 <tests>
189 <test>
190 <!--
191 BWA commands:
192 bwa aln -t 4 phiX.fasta test-data/bwa_wrapper_in1.fastqsanger > bwa_wrapper_out1.sai
193 bwa samse phiX.fasta bwa_wrapper_out1.sai test-data/bwa_wrapper_in1.fastqsanger > bwa_wrapper_out1.sam
194 phiX.fasta is the prefix for the reference files (phiX.fasta.amb, phiX.fasta.ann, phiX.fasta.bwt, ...)
195 remove the comment lines (beginning with '@') from the resulting sam file
196 plain old sort doesn't handle underscores like python:
197 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
198 -->
199 <param name="refGenomeSource" value="indexed" />
200 <param name="indices" value="phiX" />
201 <param name="sPaired" value="single" />
202 <param name="input1" value="bwa_wrapper_in1.fastqsanger" ftype="fastqsanger" />
203 <param name="source_select" value="pre_set" />
204 <param name="suppressHeader" value="true" />
205 <output name="output" file="bwa_wrapper_out1.sam" ftype="sam" sort="True" />
206 </test>
207 <test>
208 <!--
209 BWA commands:
210 cp test-data/phiX.fasta phiX.fasta
211 bwa index -a is phiX.fasta
212 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
213 bwa samse -n 3 phiX.fasta bwa_wrapper_out2.sai test-data/bwa_wrapper_in1.fastqsanger > bwa_wrapper_out2.u.sam
214 phiX.fasta is the prefix for the reference files (phiX.fasta.amb, phiX.fasta.ann, phiX.fasta.bwt, ...)
215 remove the comment lines (beginning with '@') from the resulting sam file
216 plain old sort doesn't handle underscores like python:
217 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
218 -->
219 <param name="refGenomeSource" value="history" />
220 <param name="ownFile" value="phiX.fasta" />
221 <param name="sPaired" value="single" />
222 <param name="input1" value="bwa_wrapper_in1.fastqsanger" ftype="fastqsanger" />
223 <param name="source_select" value="full" />
224 <param name="maxEditDist" value="0" />
225 <param name="fracMissingAligns" value="0.04" />
226 <param name="maxGapOpens" value="1" />
227 <param name="maxGapExtens" value="-1" />
228 <param name="disallowLongDel" value="16" />
229 <param name="disallowIndel" value="5" />
230 <param name="seed" value="-1" />
231 <param name="maxEditDistSeed" value="2" />
232 <param name="mismatchPenalty" value="3" />
233 <param name="gapOpenPenalty" value="11" />
234 <param name="gapExtensPenalty" value="4" />
235 <param name="suboptAlign" value="" />
236 <param name="noIterSearch" value="true" />
237 <param name="outputTopN" value="3" />
238 <param name="outputTopNDisc" value="10" />
239 <param name="maxInsertSize" value="500" />
240 <param name="maxOccurPairing" value="100000" />
241 <param name="specReadGroup" value="no" />
242 <param name="suppressHeader" value="true" />
243 <output name="output" file="bwa_wrapper_out2.sam" ftype="sam" sort="True" />
244 </test>
245 <test>
246 <!--
247 BWA commands:
248 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
249 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
250 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
251 phiX.fasta is the prefix for the reference
252 plain old sort doesn't handle underscores like python:
253 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
254 -->
255 <param name="refGenomeSource" value="indexed" />
256 <param name="indices" value="phiX" />
257 <param name="sPaired" value="paired" />
258 <param name="input1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
259 <param name="input2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" />
260 <param name="source_select" value="full" />
261 <param name="maxEditDist" value="0" />
262 <param name="fracMissingAligns" value="0.04" />
263 <param name="maxGapOpens" value="1" />
264 <param name="maxGapExtens" value="-1" />
265 <param name="disallowLongDel" value="16" />
266 <param name="disallowIndel" value="5" />
267 <param name="seed" value="-1" />
268 <param name="maxEditDistSeed" value="2" />
269 <param name="mismatchPenalty" value="3" />
270 <param name="gapOpenPenalty" value="11" />
271 <param name="gapExtensPenalty" value="4" />
272 <param name="suboptAlign" value="" />
273 <param name="noIterSearch" value="true" />
274 <param name="outputTopN" value="3" />
275 <param name="outputTopNDisc" value="10" />
276 <param name="maxInsertSize" value="500" />
277 <param name="maxOccurPairing" value="100000" />
278 <param name="specReadGroup" value="yes" />
279 <param name="rgid" value="abcdefg" />
280 <param name="rgcn" value="" />
281 <param name="rgds" value="descrip" />
282 <param name="rgdt" value="2010-11-01" />
283 <param name="rgfo" value="" />
284 <param name="rgks" value="" />
285 <param name="rglb" value="lib-mom-A" />
286 <param name="rgpg" value="" />
287 <param name="rgpi" value="400" />
288 <param name="rgpl" value="ILLUMINA" />
289 <param name="rgpu" value="" />
290 <param name="rgsm" value="mom" />
291 <param name="suppressHeader" value="false" />
292 <output name="output" file="bwa_wrapper_out3.sam" ftype="sam" sort="True" lines_diff="2" />
293 </test>
294 <test>
295 <!--
296 BWA commands:
297 cp test-data/phiX.fasta phiX.fasta
298 bwa index -a is phiX.fasta
299 bwa aln -t 4 phiX.fasta test-data/bwa_wrapper_in2.fastqsanger > bwa_wrapper_out8a.sai
300 bwa aln -t 4 phiX.fasta test-data/bwa_wrapper_in3.fastqsanger > bwa_wrapper_out8b.sai
301 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
302 phiX.fa is the prefix for the reference
303 remove the comment lines (beginning with '@') from the resulting sam file
304 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
305 -->
306 <param name="refGenomeSource" value="history" />
307 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
308 <param name="ownFile" value="phiX.fasta" />
309 <param name="sPaired" value="paired" />
310 <param name="input1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
311 <param name="input2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" />
312 <param name="source_select" value="preSet" />
313 <param name="suppressHeader" value="true" />
314 <output name="output" file="bwa_wrapper_out8.sam" ftype="sam" sort="True" />
315 </test>
316 </tests>
317 <help>
318
319 **What it does**
320
321 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.
322
323 ------
324
325 **Know what you are doing**
326
327 .. class:: warningmark
328
329 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.
330
331 .. __: http://bio-bwa.sourceforge.net/
332
333 ------
334
335 **Input formats**
336
337 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.
338
339 ------
340
341 **A Note on Built-in Reference Genomes**
342
343 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.
344
345 ------
346
347 **Outputs**
348
349 The output is in SAM format, and has the following columns::
350
351 Column Description
352 -------- --------------------------------------------------------
353 1 QNAME Query (pair) NAME
354 2 FLAG bitwise FLAG
355 3 RNAME Reference sequence NAME
356 4 POS 1-based leftmost POSition/coordinate of clipped sequence
357 5 MAPQ MAPping Quality (Phred-scaled)
358 6 CIGAR extended CIGAR string
359 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
360 8 MPOS 1-based Mate POSition
361 9 ISIZE Inferred insert SIZE
362 10 SEQ query SEQuence on the same strand as the reference
363 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
364 12 OPT variable OPTional fields in the format TAG:VTYPE:VALU
365
366 The flags are as follows::
367
368 Flag Description
369 ------ -------------------------------------
370 0x0001 the read is paired in sequencing
371 0x0002 the read is mapped in a proper pair
372 0x0004 the query sequence itself is unmapped
373 0x0008 the mate is unmapped
374 0x0010 strand of the query (1 for reverse)
375 0x0020 strand of the mate
376 0x0040 the read is the first read in a pair
377 0x0080 the read is the second read in a pair
378 0x0100 the alignment is not primary
379
380 It looks like this (scroll sideways to see the entire example)::
381
382 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
383 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
384 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
385
386 -------
387
388 **BWA settings**
389
390 All of the options have a default value. You can change any of them. All of the options in BWA have been implemented here.
391
392 ------
393
394 **BWA parameter list**
395
396 This is an exhaustive list of BWA options:
397
398 For **aln**::
399
400 -n NUM Maximum edit distance if the value is INT, or the fraction of missing
401 alignments given 2% uniform base error rate if FLOAT. In the latter
402 case, the maximum edit distance is automatically chosen for different
403 read lengths. [0.04]
404 -o INT Maximum number of gap opens [1]
405 -e INT Maximum number of gap extensions, -1 for k-difference mode
406 (disallowing long gaps) [-1]
407 -d INT Disallow a long deletion within INT bp towards the 3'-end [16]
408 -i INT Disallow an indel within INT bp towards the ends [5]
409 -l INT Take the first INT subsequence as seed. If INT is larger than the
410 query sequence, seeding will be disabled. For long reads, this option
411 is typically ranged from 25 to 35 for '-k 2'. [inf]
412 -k INT Maximum edit distance in the seed [2]
413 -t INT Number of threads (multi-threading mode) [1]
414 -M INT Mismatch penalty. BWA will not search for suboptimal hits with a score
415 lower than (bestScore-misMsc). [3]
416 -O INT Gap open penalty [11]
417 -E INT Gap extension penalty [4]
418 -c Reverse query but not complement it, which is required for alignment
419 in the color space.
420 -R Proceed with suboptimal alignments even if the top hit is a repeat. By
421 default, BWA only searches for suboptimal alignments if the top hit is
422 unique. Using this option has no effect on accuracy for single-end
423 reads. It is mainly designed for improving the alignment accuracy of
424 paired-end reads. However, the pairing procedure will be slowed down,
425 especially for very short reads (~32bp).
426 -N Disable iterative search. All hits with no more than maxDiff
427 differences will be found. This mode is much slower than the default.
428
429 For **samse**::
430
431 -n INT Maximum number of alignments to output in the XA tag for reads paired
432 properly. If a read has more than INT hits, the XA tag will not be
433 written. [3]
434 -r STR Specify the read group in a format like '@RG\tID:foo\tSM:bar' [null]
435
436 For **sampe**::
437
438 -a INT Maximum insert size for a read pair to be considered as being mapped
439 properly. Since version 0.4.5, this option is only used when there
440 are not enough good alignment to infer the distribution of insert
441 sizes. [500]
442 -n INT Maximum number of alignments to output in the XA tag for reads paired
443 properly. If a read has more than INT hits, the XA tag will not be
444 written. [3]
445 -N INT Maximum number of alignments to output in the XA tag for disconcordant
446 read pairs (excluding singletons). If a read has more than INT hits,
447 the XA tag will not be written. [10]
448 -o INT Maximum occurrences of a read for pairing. A read with more
449 occurrences will be treated as a single-end read. Reducing this
450 parameter helps faster pairing. [100000]
451 -r STR Specify the read group in a format like '@RG\tID:foo\tSM:bar' [null]
452
453 For specifying the read group in **samse** or **sampe**, use the following::
454
455 @RG Read group. Unordered multiple @RG lines are allowed.
456 ID Read group identifier. Each @RG line must have a unique ID. The value of
457 ID is used in the RG tags of alignment records. Must be unique among all
458 read groups in header section. Read group IDs may be modified when
459 merging SAM files in order to handle collisions.
460 CN Name of sequencing center producing the read.
461 DS Description.
462 DT Date the run was produced (ISO8601 date or date/time).
463 FO Flow order. The array of nucleotide bases that correspond to the
464 nucleotides used for each flow of each read. Multi-base flows are encoded
465 in IUPAC format, and non-nucleotide flows by various other characters.
466 Format : /\*|[ACMGRSVTWYHKDBN]+/
467 KS The array of nucleotide bases that correspond to the key sequence of each read.
468 LB Library.
469 PG Programs used for processing the read group.
470 PI Predicted median insert size.
471 PL Platform/technology used to produce the reads. Valid values : CAPILLARY,
472 LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO.
473 PU Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for
474 SOLiD). Unique identifier.
475 SM Sample. Use pool name where a pool is being sequenced.
476
477 </help>
478 </tool>
479
480