bwa_wrapper.py --threads="4" #if $genomeSource.refGenomeSource == "history": --ref=$genomeSource.ownFile #else: --ref=$genomeSource.indices #end if --fastq=$paired.input1 #if $paired.sPaired == "paired": --rfastq=$paired.input2 #else: --rfastq="None" #end if --output=$output --genAlignType=$paired.sPaired --params=$params.source_select --fileSource=$genomeSource.refGenomeSource #if $params.source_select == "pre_set": --maxEditDist="None" --fracMissingAligns="None" --maxGapOpens="None" --maxGapExtens="None" --disallowLongDel="None" --disallowIndel="None" --seed="None" --maxEditDistSeed="None" --mismatchPenalty="None" --gapOpenPenalty="None" --gapExtensPenalty="None" --suboptAlign="None" --noIterSearch="None" --outputTopN="None" --maxInsertSize="None" --maxOccurPairing="None" #else: --maxEditDist=$params.maxEditDist --fracMissingAligns=$params.fracMissingAligns --maxGapOpens=$params.maxGapOpens --maxGapExtens=$params.maxGapExtens --disallowLongDel=$params.disallowLongDel --disallowIndel=$params.disallowIndel --seed=$params.seed --maxEditDistSeed=$params.maxEditDistSeed --mismatchPenalty=$params.mismatchPenalty --gapOpenPenalty=$params.gapOpenPenalty --gapExtensPenalty=$params.gapExtensPenalty --suboptAlign=$params.suboptAlign --noIterSearch=$params.noIterSearch --outputTopN=$params.outputTopN --maxInsertSize=$params.maxInsertSize --maxOccurPairing=$params.maxOccurPairing #end if #if $genomeSource.refGenomeSource == "history": --dbkey=$dbkey #else: --dbkey="None" #end if --suppressHeader=$suppressHeader bwa Use a built-in index Use one from the history Single-end Paired-end Commonly Used Full Parameter List

**What it does** 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. ------ **Know what you are doing** .. class:: warningmark 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. .. __: http://bio-bwa.sourceforge.net/ ------ **Input formats** BWA accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files. ------ **Outputs** The output is in SAM format, and has the following columns:: Column Description -------- -------------------------------------------------------- 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. NOTE: Entering a value other than -1 will result in output that is not in SAM format, and therefore not usable further down the pipeline. Check the BWA documentation for details on the format of the output. [-1] For **sampe**:: -a INT Maximum insert size for a read pair to be considered as being mapped properly. Since version 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]