MAQ(1)							       Bioinformatics Tools							    MAQ(1)

NAME

       Maq - Mapping and Assembly with Qualities

SYNOPSIS

       maq command [options] arguments

       maq.pl command [options] arguments

DESCRIPTION

       Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. It is particularly
       designed for Illumina-Solexa 1G Genetic Analyzer, and has a preliminary functionality to handle AB SOLiD data.

       With Maq you can:

       o Fast align Illumina/SOLiD reads to the reference genome. With the default options, one million pairs of reads can be mapped to the human
	 genome in about 10 CPU hours with less than 1G memory.

       o Accurately measure the error probability of the alignment of each individual read.

       o Call the consensus genotypes, including homozygous and heterozygous polymorphisms, with a Phred probabilistic quality assigned to each
	 base.

       o Find short indels with paired end reads.

       o Accurately find large scale genomic deletions and translocations with paired end reads.

       o Discover potential CNVs by checking read depth.

       o Evaluate the accuracy of raw base qualities from sequencers and help to check the systematic errors.

       However, Maq can NOT:

       o Do de novo assembly. (Maq can only call the consensus by mapping reads to a known reference.)

       o Map shorts reads against themselves. (Maq can only find complete overlap between reads.)

       o Align capillary reads or 454 reads to the reference. (Maq cannot align reads longer than 63bp.)

MAQ COMMANDS

       Key Commands

       fasta2bfa  maq fasta2bfa in.ref.fasta out.ref.bfa

		  Convert sequences in FASTA format to Maq's BFA (binary FASTA) format.

       fastq2bfq  maq fastq2bfq [-n nreads] in.read.fastq out.read.bfq|out.prefix

		  Convert reads in FASTQ format to Maq's BFQ (binary FASTQ) format.

		  OPTIONS:

		  -n INT   number of reads per file [not specified]

       map	  maq map [-n nmis] [-a maxins] [-c] [-1 len1] [-2 len2] [-d adap3] [-m mutrate] [-u unmapped] [-e maxerr] [-M c|g] [-N] [-H all-
		  hits] [-C maxhits] out.aln.map in.ref.bfa in.read1.bfq [in.read2.bfq] 2> out.map.log

		  Map reads to the reference sequences.

		  OPTIONS:

		  -n INT   Number of maximum mismatches that can always be found [2]

		  -a INT   Maximum outer distance for a correct read pair [250]

		  -A INT   Maximum outer distance of two RF paied read (0 for disable) [0]

		  -c	   Map reads in the colour space (for SOLiD only)

		  -1 INT   Read length for the first read, 0 for auto [0]

		  -2 INT   Read length for the second read, 0 for auto [0]

		  -m FLOAT Mutation rate between the reference sequences and the reads [0.001]

		  -d FILE  Specify a file containing a single line of the 3'-adapter sequence [null]

		  -u FILE  Dump unmapped reads and reads containing more than nmis mismatches to a separate file [null]

		  -e INT   Threshold on the sum of mismatching base qualities [70]

		  -H FILE  Dump multiple/all 01-mismatch hits to FILE [null]

		  -C INT   Maximum number of hits to output. Unlimited if larger than 512. [250]

		  -M c|g   methylation alignment mode. All C (or G) on the forward strand will be changed to T (or A). This option is for testing
			   only.

		  -N	   store the mismatch position in the output file out.aln.map. When this option is in use, the maximum allowed read length
			   is 55bp.

		  NOTE:

		  * Paired end reads should be prepared in two files, one for each end, with reads are sorted in the same order. This means the
		    k-th read in the first file is mated with the k-th read in the second file. The corresponding read names must be identical up
		    to the tailing `/1' or `/2'. For example, such a pair of read names are allowed: `EAS1_1_5_100_200/1' and
		    `EAS1_1_5_100_200/2'. The tailing `/[12]' is usually generated by the GAPipeline to distinguish the two ends in a pair.

		  * The output is a compressed binary file. It is affected by the endianness.

		  * The best way to run this command is to provide about 1 to 3 million reads as input. More reads consume more memory.

		  * Option -n controls the sensitivity of the alignment. By default, a hit with up to 2 mismatches can be always found. Higher -n
		    finds more hits and also improves the accuracy of mapping qualities. However, this is done at the cost of speed.

		  * Alignments with many high-quality mismatches should be discarded as false alignments or possible contaminations. This behav-
		    iour is controlled by option -e. The -e threshold is only calculated approximately because base qualities are divided by 10 at
		    a certain stage of the alignment. The -Q option in the assemble command precisely set the threshold.

		  * A pair of reads are said to be correctly paired if and only if the orientation is FR and the outer distance of the pair is no
		    larger than maxins. There is no limit on the minimum insert size. This setting is determined by the paired end alignment algo-
		    rithm used in Maq. Requiring a minimum insert size will lead to some wrong alignments with highly overestimated mapping quali-
		    ties.

		  * Currently, read pairs from Illumina/Solexa long-insert library have RF read orientation. The maximum insert size is set by
		    option -A. However, long-insert library is also mixed with a small fraction of short-insert read pairs. -a should also be set
		    correctly.

		  * Sometimes 5'-end or even the entire 3'-adapter sequence may be sequenced. Providing -d renders Maq to eliminate the adapter
		    contaminations.

		  * Given 2 million reads as input, maq usually takes 800MB memory.

       mapmerge   maq mapmerge out.aln.map in.aln1.map in.aln2.map [...]

		  Merge a batch of read alignments together.

		  NOTE:

		  * In theory, this command can merge unlimited number of alignments. However, as mapmerge will be reading all the inputs at the
		    same time, it may hit the limit of the maximum number of opening files set by the OS. At present, this has to be manually
		    solved by endusers.

		  * Command mapmerge can be used to merge alignment files with different read lengths. All the subsequent analyses do not assume
		    fixed length any more.

       rmdup	  maq rmdup out.rmdup.map in.ori.map

		  Remove pairs with identical outer coordinates. In principle, pairs with identical outer coordinates should happen rarely. How-
		  ever, due to the amplification in sample preparation, this occurs much more frequently than by chance. Practical analyses show
		  that removing duplicates helps to improve the overall accuracy of SNP calling.

       assemble   maq assemble [-sp] [-m maxmis] [-Q maxerr] [-r hetrate] [-t coef] [-q minQ] [-N nHap] out.cns in.ref.bfa in.aln.map 2>
		  out.cns.log

		  Call the consensus sequences from read mapping.

		  OPTIONS:

		  -t FLOAT Error dependency coefficient [0.93]

		  -r FLOAT Fraction of heterozygotes among all sites [0.001]

		  -s	   Take single end mapping quality as the final mapping quality; otherwise paired end mapping quality will be used

		  -p	   Discard paired end reads that are not mapped in correct pairs

		  -m INT   Maximum number of mismatches allowed for a read to be used in consensus calling [7]

		  -Q INT   Maximum allowed sum of quality values of mismatched bases [60]

		  -q INT   Minimum mapping quality allowed for a read to be used in consensus calling [0]

		  -N INT   Number of haplotypes in the pool (>=2) [2]

		  NOTE:

		  * Option -Q sets a limit on the maximum sum of mismatching base qualities. Reads containing many high-quality mismatches should
		    be discarded.

		  * Option -N sets the number of haplotypes in a pool. It is designed for resequencing of samples by pooling multiple
		    strains/individuals together. For diploid genome resequencing, this option equals 2.

       glfgen	  maq glfgen [-sp] [-m maxmis] [-Q maxerr] [-r hetrate] [-t coef] [-q minQ] [-N nHap] out.cns in.ref.bfa in.aln.map 2> out.cns.log

		  Calculate log-likelihood for all genotypes and store the results in GLF format (Genotyping Likelihood Format). Please check MAQ
		  website for detailed descriptions of the file format and the related utilities.

       indelpe	  maq indelpe in.ref.bfa in.aln.map > out.indelpe

		  Call consistent indels from paired end reads. The output is TAB delimited with each line consisting of chromosome, start posi-
		  tion, type of the indel, number of reads across the indel, size of the indel and inserted/deleted nucleotides (separated by
		  colon), number of indels on the reverse strand, number of indels on the forward strand, 5' sequence ahead of the indel, 3'
		  sequence following the indel, number of reads aligned without indels and three additional columns for filters.

		  At the 3rd column, type of the indel, a star indicates the indel is confirmed by reads from both strands, a plus means the indel
		  is hit by at least two reads but from the same strand, a minus shows the indel is only found on one read, and a dot means the
		  indel is too close to another indel and is filtered out.

		  Users are recommended to run through `maq.pl indelpe' to correct the number of reads mapped without indels. For more details,
		  see the `maq.pl indelpe' section.

       indelsoa   maq indelsoa in.ref.bfa in.aln.map > out.indelsoa

		  Call potential homozygous indels and break points by detecting the abnormal alignment pattern around indels and break points.
		  The output is also TAB delimited with each line consisting of chromosome, approximate coordinate, length of the abnormal region,
		  number of reads mapped across the position, number of reads on the left-hand side of the position and number of reads on the
		  right-hand side. The last column can be ignored.

		  The output contains many false positives. A recommended filter could be:

		    awk '$5+$6-$4 >= 3 && $4 <= 1' in.indelsoa

		  Note that this command does not aim to be an accurate indel detector, but mainly helps to avoid some false positives in substi-
		  tution calling. In addition, it only works well given deep depth (~40X for example); otherwise the false negative rate would be
		  very high.

       Format Converting

       sol2sanger maq sol2sanger in.sol.fastq out.sanger.fastq

		  Convert Solexa FASTQ to standard/Sanger FASTQ format.

       bfq2fastq  maq bfq2fastq in.read.bfq out.read.fastq

		  Convert Maq's BFQ format to standard FASTQ format.

       mapass2maq maq mapass2maq in.mapass2.map out.maq.map

		  Convert obsolete mapass2's map format to Maq's map format. The old format does not contain read names.

       Information Extracting

       mapview	  maq mapview [-bN] in.aln.map > out.aln.txt

		  Display the read alignment in plain text. For reads aligned before the Smith-Waterman alignment, each line consists of read
		  name, chromosome, position, strand, insert size from the outer coorniates of a pair, paired flag, mapping quality, single-end
		  mapping quality, alternative mapping quality, number of mismatches of the best hit, sum of qualities of mismatched bases of the
		  best hit, number of 0-mismatch hits of the first 24bp, number of 1-mismatch hits of the first 24bp on the reference, length of
		  the read, read sequence and its quality.  Alternative mapping quality always equals to mapping quality if the reads are not
		  paired. If reads are paired, it equals to the smaller mapping quality of the two ends. This alternative mapping quality is actu-
		  ally the mapping quality of an abnormal pair.

		  The fifth column, paired flag, is a bitwise flag. Its lower 4 bits give the orientation: 1 stands for FF, 2 for FR, 4 for RF,
		  and 8 for RR, where FR means that the read with smaller coordinate is on the forward strand, and its mate is on the reverse
		  strand. Only FR is allowed for a correct pair. The higher bits of this flag give further information. If the pair meets the
		  paired end requirement, 16 will be set. If the two reads are mapped to different chromosomes, 32 will be set. If one of the two
		  reads cannot be mapped at all, 64 will be set. The flag for a correct pair always equals to 18.

		  For reads aligned by the Smith-Waterman alignment afterwards, the flag is always 130. A line consists of read name, chromosome,
		  position, strand, insert size, flag (always 130), position of the indel on the read (0 if no indel), length of the indels (posi-
		  tive for insertions and negative for deletions), mapping quality of its mate, number of mismatches of the best hit, sum of qual-
		  ities of mismatched bases of the best hit, two zeros, length of the read, read sequence and its quality. The mate of a
		  130-flagged read always gets a flag 18.

		  Flag 192 indicates that the read is not mapped but its mate is mapped. For such a read pair, one read has flag 64 and the other
		  has 192.

		  OPTIONS:

		  -b	   do not display the read sequence and the quality

		  -N	   display the positions where mismatches occur. This flag only works with a .map file generated by `maq map -N'.

       mapcheck   maq mapcheck [-s] [-m maxmis] [-q minQ] in.ref.bfa in.aln.map > out.mapcheck

		  Read quality check. The mapcheck first reports the composition and the depth of the reference. After that there is a form. The
		  first column indicates the position on a read. Following four columns which show the nucleotide composition, substitution rates
		  between the reference and reads will be given. These rates and the numbers in the following columns are scaled to 999 and
		  rounded to nearest integer. The next group of columns show the distribution of base qualities along the reads at a quality
		  interval of 10. A decay in quality can usually be observed, which means bases at the end of read are less accurate. The last
		  group of columns present the fraction of substitutions for read bases at a quality interval. This measures the accuracy of base
		  quality estimation. Idealy, we expect to see 1 in the 3? column, 10 in the 2?  column and 100 in the 1? column.

		  OPTIONS:

		  -s	   Take single end mapping quality as the final mapping quality

		  -m INT   Maximum number of mismatahces allowed for a read to be counted [4]

		  -q INT   Minimum mapping quality allowed for a read to be counted [30]

       pileup	  maq pileup [-spvP] [-m maxmis] [-Q maxerr] [-q minQ] [-l sitefile] in.ref.bfa in.aln.map > out.pileup

		  Display the alignment in a `pileup' text format. Each line consists of chromosome, position, reference base, depth and the bases
		  on reads that cover this position. If -v is added on the command line, base qualities and mapping qualities will be presented in
		  the sixth and seventh columns in order.

		  The fifth column always starts with `@'. In this column, read bases identical to the reference are showed in comma `,' or dot
		  `.', and read bases different from the reference in letters. A comma or a upper case indicates that the base comes from a read
		  aligned on the forward strand, while a dot or a lower case on the reverse strand.

		  This command is for users who want to develop their own SNP callers.

		  OPTIONS:

		  -s	   Take single end mapping quality as the final mapping quality

		  -p	   Discard paired end reads that are not mapped as correct pairs

		  -v	   Output verbose information including base qualities and mapping qualities

		  -m INT   Maximum number of mismatches allowed for a read to be used [7]

		  -Q INT   Maximum allowed number of quality values of mismatches [60]

		  -q INT   Minimum mapping quality allowed for a read to be used [0]

		  -l FILE  File containing the sites at which pileup will be printed out. In this file the first column gives the names of the
			   reference and the second the coordinates. Additional columns will be ignored. [null]

		  -P	   also output the base position on the read

       cns2fq	  maq cns2fq [-Q minMapQ] [-n minNeiQ] [-d minDepth] [-D maxDepth] in.cns > out.cns.fastq

		  Extract the consensus sequences in FASTQ format. In the sequence lines, bases in lower case are essentially repeats or do not
		  have sufficient coverage; bases in upper case indicate regions where SNPs can be reliably called. In the quality lines, ASCII of
		  a character minus 33 gives the PHRED quality.

		  OPTIONS:

		  -Q INT   Minimum mapping quality [40]

		  -d INT   Minimum read depth [3]

		  -n INT   Minimum neighbouring quality [20]

		  -D INT   Maximum read dpeth. >=255 for unlimited. [255]

       cns2snp	  maq cns2snp in.cns > out.snp

		  Extract SNP sites. Each line consists of chromosome, position, reference base, consensus base, Phred-like consensus quality,
		  read depth, the average number of hits of reads covering this position, the highest mapping quality of the reads covering the
		  position, the minimum consensus quality in the 3bp flanking regions at each side of the site (6bp in total), the second best
		  call, log likelihood ratio of the second best and the third best call, and the third best call.

		  The 5th column is the key criterion when you judge the reliability of a SNP. However, as this quality is only calculated assum-
		  ing site independency, you should also consider other columns to get more accurate SNP calls. Script command `maq.pl SNPfilter'
		  is designed for this (see below).

		  The 7th column implies whether the site falls in a repetitive region. If no read covering the site can be mapped with high map-
		  ping quality, the flanking region is possibly repetitive or in the lack of good reads. A SNP at such site is usually not reli-
		  able.

		  The 8th column roughly gives the copy number of the flanking region in the reference genome. In most cases, this number
		  approaches 1.00, which means the region is about unique. Sometimes you may see non-zero read depth but 0.00 at the 7th column.
		  This indicates that all the reads covering the position have at least two mismatches. Maq only counts the number of 0- and
		  1-mismatch hits to the reference. This is due to a complex technical issue.

		  The 9th column gives the neighbouring quality. Filtering on this column is also required to get reliable SNPs. This idea is
		  inspired by NQS, although NQS is initially designed for a single read instead of a consensus.

       cns2view   maq cns2view in.cns > out.view

		  Show detailed information at all sites. The output format is identical to cns2snp report.

       cns2ref	  maq cns2ref in.cns > out.ref.fasta

		  Extract the reference sequence.

       cns2win	  maq cns2win [-w winsize] [-c chr] [-b begin] [-e end] [-q minQ] in.cns > out.win

		  Extract information averaged in a tilling window. The output is TAB delimited, which consists of reference name, coordinate
		  divided by 1,000,000, SNP rate, het rate, raw read depth, read depth in approximately unique regions, the average number of hits
		  of reads in the window and percent GC.

		  OPTIONS:

		  -w INT   Size of a window [1000]

		  -c STR   Destinated reference sequence; otherwise all references will be used [null]

		  -b INT   Start position, 0 for no constraint [0]

		  -e INT   End position, 0 for no constraint [0]

		  -q INT   Minimum consensus quality of the sites to be used [0]

       Simulation Related

       fakemut	  maq fakemut [-r mutrate] [-R indelfrac] in.ref.fasta > out.fakeref.fasta 2> out.fake.snp

		  Randomly introduce substitutions and indels to the reference. Substitutions and sinlge base-pair indels can be added.

		  OPTIONS:

		  -r FLOAT  Mutation rate [0.001]

		  -R FLOAT  Fraction of mutations to be indels [0.1]

       simutrain  maq simutrain out.simupars.dat in.read.fastq

		  Estimate/train parameters for read simulation.

       simulate   maq simulate [-d insize] [-s stdev] [-N nReads] [-1 readLen1] [-2 readLen2] [-r mutRate] [-R indelFrac] [-h] out.read1.fastq
		  out.read2.fastq in.ref.fasta in.simupars.dat

		  Simulate paired end reads. File in.simupars.dat determines the read lengths and quality distribution. It is generated from simu-
		  train, or can be downloaded from Maq website. In the output read files, a read name consists of the reference sequence name and
		  the outer coordinates of the pair of simulated reads. By default, simulate assumes reads come from a diploid sequence which is
		  generated by adding two different sets of mutations, including one base-pair indels, to in.ref.fasta.

		  OPTIONS:

		  -d INT   mean of the outer distance of insert sizes [170]

		  -s INT   standard deviation of insert sizes [20]

		  -N INT   number of pairs of reads to be generated [1000000]

		  -1 INT   length of the first read [set by in.simupars.dat]

		  -2 INT   length of the second read [set by in.simupars.dat]

		  -r FLOAT mutation rate [0.001]

		  -R FLOAT fraction of 1bp indels [0.1]

		  -h	   add all mutations to in.ref.fasta and generate reads from the single mutated sequence (haploid mode)

		  NOTE:

		  * Reads generated from this command are independent, which deviates from the truth. Whereas alignment evaluation is less
		    affected by this, evaluation on SNP calling should be performed with caution. Error dependency may be one of the major causes
		    of wrong SNP calls.

       simustat   maq simustat in.simu-aln.map > out.simustat

		  Evaluate mapping qualities from simulated reads.

       SOLiD Related

       fasta2csfa maq fasta2csfa in.nucl-ref.fasta > out.colour-ref.fasta

		  Convert nucleotide FASTA to colour-coded FASTA. Flag -c should be then applied to map command. In the output, letter `A' stands
		  for color 0, `C' for 1, `G' for 2 and `T' for 3. Each sequence in the output is 1bp shorter than the input.

       csmap2nt   maq csmap2nt out.nt.map in.ref.nt.bfa in.cs.map

		  Convert color alignment to nucleotide alignment. The input in.ref.nt.bfa is the nucleotide binary FASTA reference file. It must
		  correspond to the original file from which the color reference is converted. Nucleotide consensus can be called from the resul-
		  tant alignment.

       Miscellaneous/Advanced Commands

       submap	  maq submap [-q minMapQ] [-Q maxSumErr] [-m maxMM] [-p] out.map in.map

		  Filter bad alignments in in.map. Command-line options are described in the `assemble' command.

       eland2maq  maq eland2maq [-q defqual] out.map in.list in.eland

		  Convert eland alignment to maq's .map format. File in.list consists of the sequence names that appear at the seventh column of
		  the eland alignment file in.eland and the name you expect to see in maq alignment. The following is an example:

		    cX.fa chrX
		    c1.fa chr1
		    c2.fa chr2

		  If you are aligning reads in several batches using eland, it is important to use the same in.list for the conversion. In addi-
		  tion, maq will load all the alignments and sort them in the memory. If you have concatenate several eland outputs into one huge
		  file, you should separate it into smaller files to prevent maq from eating all your machine memory.

		  This command actually aims to show Eland alignment in Maqview. As no quality information is available, the resultant maq align-
		  ment file should not be used to call consensus genotypes.

       export2maq maq export2maq [-1 read1len] [-2 read2len] [-a maxdist] [-n] out.map in.list in.export

		  Convert Illumina's Export format to Maq's .map format. Export format is a new alignment format since SolexaPipeline-0.3.0 which
		  also calculates mapping qualities like maq. The resultant file can be used to call consensus genotypes as most of necessary
		  information is available for maq to do this accurately.

		  OPTIONS:

		  -1 INT   Length of the first read [0]

		  -2 INT   Length of the second read [0]

		  -a INT   Maximum outer distance for a correct read pair [250]

		  -n	   Retain filtered reads

MAQ-PERL COMMANDS
       demo	  maq.pl demo [-h] [-s] [-N nPairs] [-d outDir] in.fasta in.simudat

		  Demonstrate the use of maq and its companion scripts. This command will simulate reads from a FASTA file in.fasta. The sequence
		  length and qualities are determined by in.simudat which is generated from maq simutrain or can be downloaded from Maq website.
		  The simulated reads will then be mapped with maq.pl easyrun. The alignment accuracy is evaluated by maq simustat, the consensus
		  accuracy by maq simucns, and the SNP accuracy by maq_eval.pl.

		  By default, paired end reads will be simulated and a diploid sequence will be generated from the input by adding mutations to
		  either haploid type. The insert size and mutation rate are controlled by maq simulate.

		  OPTIONS:

		  -h	   simulate a haploid sequence instead of a diploid sequence

		  -s	   use single-end mode to align reads instead of paired-end mode

		  -N INT   number of pairs of reads to be simulated [1000000]

		  -d DIR   output directory [maqdemo]

		  NOTE:

		  * The output files from maq_eval.pl have not been documented, but you may make a good guess at some of these files.

		  * This command just demonstrates the use of the maq suite. The accuracy on real data is almost always lower than what you see
		    from pure simulation.

       easyrun	  maq.pl easyrun [-1 read1Len] [-d out.dir] [-n nReads] [-A 3adapter] [-e minDep] [-q minCnsQ] [-p] [-2 read2Len] [-a maxIns] [-S]
		  [-N] in.ref.fasta in1.fastq [in2.fastq]

		  Analyses pipeline for small genomes. Easyrun command will run most of analyses implemented in maq. By default, easyrun assumes
		  all the input read sequences files are single-end and independent; when -p is specified, two read sequence files are required,
		  one for each end.

		  Several files will be generated in out.dir, among which the following files are the key output:

		  cns.final.snp   final SNP calls with low quality ones filtered out

		  cns.fq	  consensus sequences and qualities in the FASTQ format

		  OPTIONS:

		  -d DIR   output directory [easyrun]

		  -n INT   number of reads/pairs in one batch of alignment [2000000]

		  -S	   apply split-read analysis of short indels (maybe very slow)

		  -N INT   number of haplotypes/strains in the pool (>=2) [2]

		  -A FILE  file for 3'-adapter. The file should contain a single line of sequence [null]

		  -1 INT   length of the first read, 0 for auto [0]

		  -e INT   minimum read depth required to call a SNP (for SNPfilter) [3]

		  -q INT   minimum consensus quality for SNPs in cns.final.snp [30]

		  -p	   switch to paired end alignment mode

		  -2 INT   length of the second read when -p is applied [0]

		  -a INT   maximum insert size when -p is applied [250]

		  NOTES:

		  * For SNP calling on pooled samples, users should set correct `-N' as well as `-E 0'.

		  * The input file can be maq's binary format. maq.pl will automatically detect the file format.

       SNPfilter  maq.pl SNPfilter [-d minDep] [-D maxDep] [-Q maxMapQ] [-q minCnsQ] [-w indelWinSize] [-n minNeiQ] [-F in.indelpe] [-f in.indel-
		  soa] [-s minScore] [-m maxAcross] [-a] [-N maxWinSNP] [-W densWinSize] in.cns2snp.snp > out.filtered.snp

		  Rule out SNPs that are covered by few reads (specified by -d), by too many reads (specified by -D), near (specified by -w) to a
		  potential indel, falling in a possible repetitve region (characterized by -Q), or having low-quality neighbouring bases (speci-
		  fied by -n). If maxWinSNP or more SNPs appear in any densWinSize window, they will also be filtered out together.

		  OPTIONS:

		  -d INT    Minimum read depth required to call a SNP [3]

		  -D INT    Maximum read depth required to call a SNP (<255, otherwise ignored) [256]

		  -Q INT    Required maximum mapping quality of reads covering the SNP [40]

		  -q INT    Minimum consensus quality [20]

		  -n INT    Minimum adjacent consensus quality [20]

		  -w INT    Size of the window around the potential indels. SNPs that are close to indels will be suppressed [3]

		  -F FILE   The indelpe output [null]

		  -f FILE   The indelsoa output [null]

		  -s INT    Minimum score for a soa-indel to be considered [3]

		  -m INT    Maximum number of reads that can be mapped across a soa-indel [1]

		  -a	    Alternative filter for single end alignment

       indelpe	  maq.pl indelpe in.indelpe > out.indelpe

		  Correct the number of reads mapped without indels for homopolymer tracts. This command modify the 4th, 10th and the last three
		  columns of in.indelpe and output the result in out.indelpe. After the correction, the following awk command gives putative
		  homozygous indels:

		    awk '($3=="*"||$3=="+") && $6+$7>=3 && ($6+$7)/$4>=0.75'

		  and the following gives heterozygotes:

		    awk '($3=="*"||$3=="+") && $6+$7>=3 && ($6+$7)/$4<0.75'

		  Please note that this indelpe command just implements several heuristic rules. It does not correct for impure homopolymer runs
		  or di-nucleotide/triplet repeats. Consequently, the two awk commands only give approximate hom/het indels.

EXAMPLES

       o Easyrun script:
	   maq.pl easyrun -d easyrun ref.fasta part1.fastq part2.fastq

       o Key commands behind easyrun:
	   maq fasta2bfa ref.fasta ref.bfa;
	   maq fastq2bfq part1.fastq part1.bfq;
	   maq fastq2bfq part2.fastq part2.bfq;
	   maq map part1.map ref.bfa part1.bfq;
	   maq map part2.map ref.bfa part2.bfq;
	   maq mapmerge aln.map part1.map part2.map;
	   maq assemble cns.cns ref.bfa aln.map;

LICENSE

       GNU General Public License, version 3 (GPLv3)

AVAILABILITY

       <http://maq.sourceforge.net>

AUTHOR

       Heng Li <lh3@sanger.ac.uk>

maq-0.7.1							    2008-09-22								    MAQ(1)