BWA COMMANDS AND OPTIONSindex 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 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, but it does not work with 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 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 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. -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_xsum_i=x+1l(INT-q_i) if q_l 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 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 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 bwasw bwa bwasw -a matchScore -b mmPen -q gapOpenPen -r gapExtPen -t nThreads -w bandWidth -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 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*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 inc