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:
- •
- 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.
- •
- Accurately measure the error probability of the alignment
of each individual read.
- •
- Call the consensus genotypes, including homozygous and
heterozygous polymorphisms, with a Phred probabilistic quality assigned to
each base.
- •
- Find short indels with paired end reads.
- •
- Accurately find large scale genomic deletions and
translocations with paired end reads.
- •
- Discover potential CNVs by checking read depth.
- •
- Evaluate the accuracy of raw base qualities from sequencers
and help to check the systematic errors.
However, Maq can
NOT:
- •
- Do de novo assembly. (Maq can only call the
consensus by mapping reads to a known reference.)
- •
- Map shorts reads against themselves. (Maq can only find
complete overlap between reads.)
- •
- 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 allhits] [-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 behaviour
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 algorithm used in
Maq. Requiring a minimum insert size will lead to some wrong alignments
with highly overestimated mapping qualities.
- *
- 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. However, 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 position, 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 substitution 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 actually 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 (positive for insertions and negative for
deletions), mapping quality of its mate, number of mismatches of the best
hit, sum of qualities 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 assuming 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 mapping quality, the
flanking region is possibly repetitive or in the lack of good reads. A SNP
at such site is usually not reliable.
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 simutrain,
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 resultant
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 addition, 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 alignment 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.indelsoa] [ -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 (specified 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¶
- •
- Easyrun script:
maq.pl easyrun -d easyrun ref.fasta part1.fastq part2.fastq
- •
- 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>
