/tools/sr_mapping/bwa_wrapper.xml
XML | 474 lines | 389 code | 44 blank | 41 comment | 0 complexity | 00a9cbfaf448329ad7eb00a6d91df57a MD5 | raw file
1<tool id="bwa_wrapper" name="Map with BWA for Illumina" version="1.2.2"> 2 <description></description> 3 <parallelism method="basic"></parallelism> 4 <command interpreter="python"> 5 bwa_wrapper.py 6 --threads="4" 7 8 #if $input1.ext == "fastqillumina": 9 --illumina1.3 10 #end if 11 12 ## reference source 13 --fileSource=$genomeSource.refGenomeSource 14 #if $genomeSource.refGenomeSource == "history": 15 ##build index on the fly 16 --ref="${genomeSource.ownFile}" 17 --dbkey=$dbkey 18 #else: 19 ##use precomputed indexes 20 --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }" 21 --do_not_build_index 22 #end if 23 24 ## input file(s) 25 --input1=$paired.input1 26 #if $paired.sPaired == "paired": 27 --input2=$paired.input2 28 #end if 29 30 ## output file 31 --output=$output 32 33 ## run parameters 34 --genAlignType=$paired.sPaired 35 --params=$params.source_select 36 #if $params.source_select != "pre_set": 37 --maxEditDist=$params.maxEditDist 38 --fracMissingAligns=$params.fracMissingAligns 39 --maxGapOpens=$params.maxGapOpens 40 --maxGapExtens=$params.maxGapExtens 41 --disallowLongDel=$params.disallowLongDel 42 --disallowIndel=$params.disallowIndel 43 --seed=$params.seed 44 --maxEditDistSeed=$params.maxEditDistSeed 45 --mismatchPenalty=$params.mismatchPenalty 46 --gapOpenPenalty=$params.gapOpenPenalty 47 --gapExtensPenalty=$params.gapExtensPenalty 48 --suboptAlign=$params.suboptAlign 49 --noIterSearch=$params.noIterSearch 50 --outputTopN=$params.outputTopN 51 --outputTopNDisc=$params.outputTopNDisc 52 --maxInsertSize=$params.maxInsertSize 53 --maxOccurPairing=$params.maxOccurPairing 54 #if $params.readGroup.specReadGroup == "yes" 55 --rgid="$params.readGroup.rgid" 56 --rgcn="$params.readGroup.rgcn" 57 --rgds="$params.readGroup.rgds" 58 --rgdt="$params.readGroup.rgdt" 59 --rgfo="$params.readGroup.rgfo" 60 --rgks="$params.readGroup.rgks" 61 --rglb="$params.readGroup.rglb" 62 --rgpg="$params.readGroup.rgpg" 63 --rgpi="$params.readGroup.rgpi" 64 --rgpl="$params.readGroup.rgpl" 65 --rgpu="$params.readGroup.rgpu" 66 --rgsm="$params.readGroup.rgsm" 67 #end if 68 #end if 69 70 ## suppress output SAM header 71 --suppressHeader=$suppressHeader 72 </command> 73 <requirements> 74 <requirement type="package">bwa</requirement> 75 </requirements> 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="boolean" truevalue="true" falsevalue="false" checked="no" label="Proceed with suboptimal alignments even if the top hit is a repeat (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 identi?er (ID). Each @RG line must have a unique ID. The value of ID is used in the RG 138tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group 139IDs may be modi?ed when merging SAM ?les 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?ow of each read." help="Optional. Multi-base ?ows are encoded in IUPAC format, and non-nucleotide ?ows by 145various 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, 151SOLID, HELICOS, IONTORRENT and PACBIO" /> 152 <param name="rgpu" type="text" size="25" label="Platform unit (PU)" help="Optional. Unique identi?er (e.g. ?owcell-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="true" /> 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="true" /> 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 315BWA 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 323There 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 331BWA 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 337Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX). 338 339------ 340 341**Outputs** 342 343The 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 360The 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 374It 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 384All 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 390This is an exhaustive list of BWA options: 391 392For **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 423For **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 430For **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 447For 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 identi?er. 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 modi?ed when 453 merging SAM ?les 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 ?ow of each read. Multi-base ?ows are encoded 459 in IUPAC format, and non-nucleotide ?ows 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. ?owcell-barcode.lane for Illumina or slide for 468 SOLiD). Unique identi?er. 469 SM Sample. Use pool name where a pool is being sequenced. 470 471 </help> 472</tool> 473 474