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NAME

bwa - Burrows-Wheeler Alignment Tool

SYNOPSIS

bwa index ref.fa
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bwa mem ref.fa reads.fq > aln-se.sam
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bwa mem ref.fa read1.fq read2.fq > aln-pe.sam
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bwa aln ref.fa short_read.fq > aln_sa.sai
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bwa samse ref.fa aln_sa.sai short_read.fq > aln-se.sam
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bwa sampe ref.fa aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln-pe.sam
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bwa bwasw ref.fa long_read.fq > aln.sam

DESCRIPTION

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.For all the algorithms, BWA first needs to construct the FM-index for the reference genome (the **index** command). Alignment algorithms are invoked with different sub-commands: **aln**/**samse**/**sampe** for BWA-backtrack, **bwasw** for BWA-SW and **mem** for the BWA-MEM algorithm.

COMMANDS AND OPTIONS

index

Usage

bwa index [-p prefix] [-a algoType] <in.db.fasta>Index database sequences in the FASTA format

OPTIONS

-p STR Prefix of the output database [same as db filename]
-a STR Algorithm for constructing BWT index. Available options are:
    is  IS linear-time algorithm for constructing suffix array. It requires 5.37N memory where N is the size of the database. IS is moderately fast, but does not work with database larger than 2GB. IS is the default algorithm due to its simplicity. The current codes for IS algorithm are reimplemented by Yuta Mori.
    bwtsw   Algorithm implemented in BWT-SW. This method works with the whole human genome.

mem

Usage

bwa mem [-aCHMpP] [-t nThreads] [-k minSeedLen] [-w bandWidth] [-d zDropoff] [-r seedSplitRatio] [-c maxOcc] [-A matchScore] [-B mmPenalty] [-O gapOpenPen] [-E gapExtPen] [-L clipPen] [-U unpairPen] [-R RGline] [-v verboseLevel] db.prefix reads.fq [mates.fq]
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Align 70bp-1Mbp query sequences with the BWA-MEM algorithm. Briefly, the algorithm works by seeding alignments with maximal exact matches (MEMs) and then extending seeds with the affine-gap Smith-Waterman algorithm (SW).
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If mates.fq file is absent and option -p is not set, this command regards input reads are single-end. If mates.fq is present, this command assumes the i-th read in reads.fq and the i-th read in mates.fq constitute a read pair. If -p is used, the command assumes the 2i-th and the (2i+1)-th read in reads.fq constitute a read pair (such input file is said to be interleaved). In this case, mates.fq is ignored. In the paired-end mode, the mem command will infer the read orientation and the insert size distribution from a batch of reads.
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The BWA-MEM algorithm performs local alignment. It may produce multiple primary alignments for different part of a query sequence. This is a crucial feature for long sequences. However, some tools such as Picard’s markDuplicates does not work with split alignments. One may consider to use option -M to flag shorter split hits as secondary.

OPTIONS

-t INT  Number of threads [1]
-k INT  Minimum seed length. Matches shorter than INT will be missed. The alignment speed is usually insensitive to this value unless it significantly deviates 20. [19]
-w INT  Band width. Essentially, gaps longer than INT will not be found. Note that the maximum gap length is also affected by the scoring matrix and the hit length, not solely determined by this option. [100]
-d INT  Off-diagonal X-dropoff (Z-dropoff). Stop extension when the difference between the best and the current extension score is above |i-j|*A+INT, where i and j are the current positions of the query and reference, respectively, and A is the matching score. Z-dropoff is similar to BLAST’s X-dropoff except that it doesn’t penalize gaps in one of the sequences in the alignment. Z-dropoff not only avoids unnecessary extension, but also reduces poor alignments inside a long good alignment. [100]
-r FLOAT    Trigger re-seeding for a MEM longer than minSeedLen*FLOAT. This is a key heuristic parameter for tuning the performance. Larger value yields fewer seeds, which leads to faster alignment speed but lower accuracy. [1.5]
-c INT  Discard a MEM if it has more than INT occurence in the genome. This is an insensitive parameter. [10000]
-P  In the paired-end mode, perform SW to rescue missing hits only but do not try to find hits that fit a proper pair.
-A INT  Matching score. [1]
-B INT  Mismatch penalty. The sequence error rate is approximately: {.75 * exp[-log(4) * B/A]}. [4]
-O INT  Gap open penalty. [6]
-E INT  Gap extension penalty. A gap of length k costs O + k*E (i.e. -O is for opening a zero-length gap). [1]
-L INT  Clipping penalty. When performing SW extension, BWA-MEM keeps track of the best score reaching the end of query. If this score is larger than the best SW score minus the clipping penalty, clipping will not be applied. Note that in this case, the SAM AS tag reports the best SW score; clipping penalty is not deducted. [5]
-U INT  Penalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as scoreRead1+scoreRead2-INT and scores a paired as scoreRead1+scoreRead2-insertPenalty. It compares these two scores to determine whether we should force pairing. [9]
-p  Assume the first input query file is interleaved paired-end FASTA/Q. See the command description for details.
-R STR  Complete read group header line. ’\t’ can be used in STR and will be converted to a TAB in the output SAM. The read group ID will be attached to every read in the output. An example is ’@RG\tID:foo\tSM:bar’. [null]
-T INT  Don’t output alignment with score lower than INT. This option only affects output. [30]
-a  Output all found alignments for single-end or unpaired paired-end reads. These alignments will be flagged as secondary alignments.
-C  Append append FASTA/Q comment to SAM output. This option can be used to transfer read meta information (e.g. barcode) to the SAM output. Note that the FASTA/Q comment (the string after a space in the header line) must conform the SAM spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output.
-H  Use hard clipping ’H’ in the SAM output. This option may dramatically reduce the redundancy of output when mapping long contig or BAC sequences.
-M  Mark shorter split hits as secondary (for Picard compatibility).
-v INT  Control the verbose level of the output. This option has not been fully supported throughout BWA. Ideally, a value 0 for disabling all the output to stderr; 1 for outputting errors only; 2 for warnings and errors; 3 for all normal messages; 4 or higher for debugging. When this option takes value 4, the output is not SAM. [3]

aln

Usage

bwa aln [-n maxDiff] [-o maxGapO] [-e maxGapE] [-d nDelTail] [-i nIndelEnd] [-k maxSeedDiff] [-l seedLen] [-t nThrds] [-cRN] [-M misMsc] [-O gapOsc] [-E gapEsc] [-q trimQual] <in.db.fasta> <in.query.fq> > <out.sai>
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Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.

OPTIONS

-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]
-R INT  Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).
-c  Reverse query but not complement it, which is required for alignment in the color space. (Disabled since 0.6.x)
-N  Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.
-q INT  Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0]
-I  The input is in the Illumina 1.3+ read format (quality equals ASCII-64).
-B INT  Length of barcode starting from the 5’-end. When INT is positive, the barcode of each read will be trimmed before mapping and will be written at the BC SAM tag. For paired-end reads, the barcode from both ends are concatenated. [0]
-b  Specify the input read sequence file is the BAM format. For paired-end data, two ends in a pair must be grouped together and options -1 or -2 are usually applied to specify which end should be mapped. Typical command lines for mapping pair-end data in the BAM format are:
bwa aln ref.fa -b1 reads.bam > 1.sai
bwa aln ref.fa -b2 reads.bam > 2.sai
bwa sampe ref.fa 1.sai 2.sai reads.bam reads.bam > aln.sam
-0  When -b is specified, only use single-end reads in mapping.
-1  When -b is specified, only use the first read in a read pair in mapping (skip single-end reads and the second reads).
-2  When -b is specified, only use the second read in a read pair in mapping.

samse

Usage

bwa samse [-n maxOcc] <in.db.fasta> <in.sai> <in.fq> > <out.sam>Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.

OPTIONS

-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]

Sampe

Usage

bwa sampe [-a maxInsSize] [-o maxOcc] [-n maxHitPaired] [-N maxHitDis] [-P] <in.db.fasta> <in1.sai> <in2.sai> <in1.fq> <in2.fq> > <out.sam>
Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly.

OPTIONS

-a INT  Maximum insert size for a read pair to be considered being mapped properly. Since 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 occurrneces will be treated as a single-end read. Reducing this parameter helps faster pairing. [100000]
-P  Load the entire FM-index into memory to reduce disk operations (base-space reads only). With this option, at least 1.25N bytes of memory are required, where N is the length of the genome.
-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]
-r STR  Specify the read group in a format like ‘@RG\tID:foo\tSM:bar’. [null]

bwasw

Usage

bwa bwasw [-a matchScore] [-b mmPen] [-q gapOpenPen] [-r gapExtPen] [-t nThreads] [-w bandWidth] [-T thres] [-s hspIntv] [-z zBest] [-N nHspRev] [-c thresCoef] <in.db.fasta> <in.fq> [mate.fq]Align query sequences in the *in.fq* file. When *mate.fq* is present, perform paired-end alignment. The paired-end mode only works for reads Illumina short-insert libraries. In the paired-end mode, BWA-SW may still output split alignments but they are all marked as not properly paired; the mate positions will not be written if the mate has multiple local hits.

OPTIONS

-a INT  Score of a match [1]
-b INT  Mismatch penalty [3]
-q INT  Gap open penalty [5]
-r INT  Gap extension penalty. The penalty for a contiguous gap of size k is q+k*r. [2]
-t INT  Number of threads in the multi-threading mode [1]
-w INT  Band width in the banded alignment [33]
-T INT  Minimum score threshold divided by a [37]
-c FLOAT    Coefficient for threshold adjustment according to query length. Given an l-long query, the threshold for a hit to be retained is a*max{T,c*log(l)}. [5.5]
-z INT  Z-best heuristics. Higher -z increases accuracy at the cost of speed. [1]
-s INT  Maximum SA interval size for initiating a seed. Higher -s increases accuracy at the cost of speed. [3]
-N INT  Minimum number of seeds supporting the resultant alignment to skip reverse alignment. [5]