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1、BWA 参数说明BWA COMMANDS AND OPTIONS index bwa index -p prefix -a algoType -c Index database sequences in the FASTA format. OPTIONS: -c Build color-space index. The input fast should be in nucleotide space. -p STR Prefix of the output database same as db filename -a STR Algorithm for constructing BWT in
2、dex. 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 alg
3、orithm are reimplemented by Yuta Mori. bAlgorithm implemented in BWT-SW. This method works wtwith the whole human genome, but it does not work with sw database smaller than 10MB and it is usually slower than IS. aln bwa aln -n maxDiff -o maxGapO -e maxGapE -d nDelTail -i nIndelEnd -k maxSeedDiff -l
4、seedLen -t nThrds -cRN -M misMsc -O gapOsc -E gapEsc -q trimQual 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 Maximum edit distance if the value
5、is INT, or the fraction of NUM 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 (
6、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 typ
7、ically 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 Mismatch penalty. BWA will not search for suboptimal hits with INT a score lower than (bestScore-misMsc). 3 -O Gap open penalty 11 INT -E INT Gap extension penalt
8、y 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 -N Reverse query but not complement
9、it, which is required for alignment in the color space. 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_xsum_i=x+1l(INT-q_i) if q_lINT where l is the
10、 original read length. 0 samse bwa samse -n maxOcc 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
11、not be written. 3 sampe bwa sampe -a maxInsSize -o maxOcc -n maxHitPaired -N maxHitDis -P Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly. OPTIONS: -a Maximum insert size for a read pair to be considered being INT mapped properly. Since 0.4
12、.5, this option is only used when there are not enough good alignment to infer the distribution of insert sizes. 500 -o Maximum occurrences of a read for pairing. A read with more INT occurrneces will be treated as a single-end read. Reducing this parameter helps faster pairing. 100000 -P Load the e
13、ntire 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 Maximum number of alignments to output in the XA tag for reads INT paired properly. If a read has more than INT hits, t
14、he XA tag will not be written. 3 -N Maximum number of alignments to output in the XA tag for INT disconcordant read pairs (excluding singletons). If a read has more than INT hits, the XA tag will not be written. 10 bwasw bwa bwasw -a matchScore -b mmPen -q gapOpenPen -r gapExtPen -t nThreads -w band
15、Width -T thres -s hspIntv -z zBest -N nHspRev -c thresCoef Align query sequences in the file. 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 mu
16、lti-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*maxT,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
