MutMap is ...
Now MutMap is updated for easier installation and utilization using Python platform.
Citation: Abe, A. et al. (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nature Biotechnol. 30:174-179.
- matplotlib
- numpy
- pandas
- seaborn (optional)
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$ mutmap -h
usage: mutmap -r <FASTA> -c <BAM | FASTQ> -b <BAM | FASTQ>
-n <INT> -o <OUT_DIR> [-T] [-e <DATABASE>]
MutMap version 2.0.3
optional arguments:
-h, --help show this help message and exit
-r , --ref Reference fasta.
-c , --cultivar fastq or bam of cultivar. If you specify
fastq, please separate pairs by commma,
e.g. -c fastq1,fastq2. You can use this
optiion multiple times
-b , --bulk fastq or bam of mutnat bulk. If you specify
fastq, please separate pairs by commma,
e.g. -b fastq1,fastq2. You can use this
optiion multiple times
-n , --N-bulk Number of individuals in mutant bulk.
-o , --out Output directory. Specified name must not
exist.
-t , --threads Number of threads. If you specify the number
below one, then, MutMap will use the threads
as many as possible. [2]
-T, --trim Trim fastq by trimmomatic.
-e , --snpEff Predicte causal variant by SnpEff. Please check
available databases in SnpEff.
-v, --version show program's version number and exit
MutMap can run from FASTQ (before or after trimming) and BAM. If you want to run MutMap from VCF, please use MutPlot (example 5). Then, please make sure that your VCF include AD format.
- Example 1 : run MutMap from FASTQ after trimming
- Example 2 : run MutMap from FASTQ before trimming
- Example 3 : run MutMap from BAM
- Example 4 : run MutMap from multiple FASTQs and BAMs
- Example 5 : run MutPlot from VCF
$ mutmap -r reference.fasta \
-c cultivar.1.fastq,cultivar.2.fastq \
-b bulk.1.fastq,bulk.2.fastq \
-n 20 \
-o example_dir
-r : reference fasta
-c : FASTQs of cultivar. Please input pair-end reads separated by comma. FASTQs can be gzipped.
-b : FASTQs of bulk. Please input pair-end reads separated by comma. FASTQs can be gzipped.
-n : number of individuals in mutant bulk.
-o : name of output directory. Specified name cannot exist.
$ mutmap -r reference.fasta \
-c cultivar.1.fastq,cultivar.2.fastq \
-b bulk.1.fastq,bulk.2.fastq \
-n 20 \
-o example_dir \
-T
-r : reference fasta
-c : FASTQs of cultivar. Please input pair-end reads separated by comma. FASTQs can be gzipped.
-b : FASTQs of bulk. Please input pair-end reads separated by comma. FASTQs can be gzipped.
-n : number of individuals in mutant bulk.
-o : name of output directory. Specified name cannot exist.
-T : trim your reads by triimomatic.
$ mutmap -r reference.fasta \
-c cultivar.bam \
-b bulk.bam \
-n 20 \
-o example_dir
-r : reference fasta
-c : BAM of cultivar.
-b : BAM of bulk.
-n : number of individuals in mutant bulk.
-o : name of output directory. Specified name cannot exist.
$ mutmap -r reference.fasta \
-c cultivar_1.1.fastq,cultivar_1.2.fastq \
-c cultivar_2.bam \
-b bulk_1.1.fastq,bulk_1.2.fastq \
-b bulk_2.bam \
-b bulk_3.bam \
-n 20 \
-o example_dir
If you specify -c multiple times, please make sure that those files include only 1 individual. On the other hand, -b can include more than 1 individuals because those are bulked samples. MutMap can automatically classify FASTQs and BAMs from whether comma exits or not. Of course, you can merge FASTQs or BAMs using cat or samtools merge before input them to MutMap.
$ mutplot -h
usage: mutplot -v <VCF> -o <OUT_DIR> -n <INT> [-w <INT>] [-s <INT>]
[-D <INT>] [-d <INT>] [-N <INT>] [-m <FLOAT>]
[-S <INT>] [-e <DATABASE>] [--igv] [--indel]
MutPlot version 0.0.3
optional arguments:
-h, --help show this help message and exit
-v , --vcf VCF which contains cultivar and mutant bulk.
-o , --out Output directory. Specified name can exist.
-n , --N-bulk Number of individuals in mutant bulk.
-w , --window Window size (kb). [2000]
-s , --step Step size (kb). [100]
-D , --max-depth Maximum depth of variants which will be used. [250]
-d , --min-depth Minimum depth of variants which will be used. [8]
-N , --N-rep Number of replicates for simulation to make
null distribution. [10000]
-m , --min-SNPindex Cutoff of minimum SNP-index for clear results. [0.3]
-S , --strand-bias Filter spurious homo genotypes in cultivar using
strand bias. If ADF (or ADR) is higher than this
cutoff when ADR (or ADF) is 0, that SNP will be
filtered out. If you want to supress this filtering,
please set this cutoff to 0. [7]
-e , --snpEff Predicte causal variant by SnpEff. Please check
available databases in SnpEff.
--igv Output IGV format file to check results on IGV.
--indel Plot SNP-index with INDEL.
--version show program's version number and exit
MutPlot is included in MutMap. MutMap run MutPlot after making VCF. Then, MutPlot will work with default parameters. If you want to change some parameters and check plots, you can retry from VCF inside of (OUT_DIR/30_vcf/mutmap.vcf.gz) like below.
$ mutplot -v OUT_DIR/30_vcf/mutmap.vcf.gz \
-o ANOTHER_DIR_NAME \
-n 20 \
-w 1000 \
-s 50
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