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
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.
Input formats
BWA accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files, set to either FASTQ Sanger or FASTQ Color Space Sanger as appropriate.
A Note on Built-in Reference Genomes
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.
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 Maximum number of alignments to output in the XA tag for reads paired
properly. If a read has more than INT hits, the XA tag will not be
written. [3]
-r STR Specify the read group in a format like '@RG\tID:foo\tSM:bar' [null]
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]
-n INT Maximum number of alignments to output in the XA tag for reads paired
properly. If a read has more than INT hits, the XA tag will not be
written. [3]
-N INT Maximum number of alignments to output in the XA tag for disconcordant
read pairs (excluding singletons). If a read has more than INT hits,
the XA tag will not be written. [10]
-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]
-r STR Specify the read group in a format like '@RG\tID:foo\tSM:bar' [null]
For specifying the read group in samse or sampe, use the following:
@RG Read group. Unordered multiple @RG lines are allowed.
ID Read group identifier. Each @RG line must have a unique ID. The value of
ID is used in the RG tags of alignment records. Must be unique among all
read groups in header section. Read group IDs may be modified when
merging SAM files in order to handle collisions.
CN Name of sequencing center producing the read.
DS Description.
DT Date the run was produced (ISO8601 date or date/time).
FO Flow order. The array of nucleotide bases that correspond to the
nucleotides used for each flow of each read. Multi-base flows are encoded
in IUPAC format, and non-nucleotide flows by various other characters.
Format : /\*|[ACMGRSVTWYHKDBN]+/
KS The array of nucleotide bases that correspond to the key sequence of each read.
LB Library.
PG Programs used for processing the read group.
PI Predicted median insert size.
PL Platform/technology used to produce the reads. Valid values : CAPILLARY,
LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO.
PU Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for
SOLiD). Unique identifier.
SM Sample. Use pool name where a pool is being sequenced.