8.2 simulate

Generating simulations

simulate is used to simulate BAM files.

8.2.1 Parameters

8.2.1.1 Input

Optional inputs :

--fasta reference Genome reference to use as input

8.2.1.2 Specific Parameters

Parameter Description Default
--chrLength length1,length2,length3 Length of chromosomes to be simulated Data is simulated for 3 chromosomes with names chr1, chr2 and chr3 with length [50000, 40000, 60000]
--depth depth1 depth2 depth3 to provide average sequencing depth for each chromosome Data is simulated for 3 chromosomes with names chr1, chr2 and chr3 with depth [10, 8, 12]
--ploidy ploidy1,ploidy2,ploidy3 Ploidy for each chromosome. ploidy 1=haploid, ploidy2 = diploid Data is simulated for 3 chromosomes with names chr1, chr2 and chr3 with ploidy [2, 1, 2]
--numReadGroup value Number of read groups (libraries) for the simulation. Data for one read group is simulated.
--sampleSize value Number of individuals for whom data is to be simulated when --type HW|HKY85|SFS is used for simulation. 1 for most models, 10 for HW
--refDiv probability Simulate data with indicated reference divergence. 0.01
--baseFreq prob,prob,prob,prob Indicate base frequencies for the simulation. The four values should add up-to 1. 0.25 for all bases
--type model Which model to use to simulate: one (Felsenstein), HKY85, pair, SFS, HW. one or HKY85 with --fasta or --sampleSize > 1
--phi values Specify specific genetic distance between individuals when data for a pair of individual is simulated. This is a required parameter when --type pair is used for simulation. required
--fracPoly value Specify the number of sites that are to be simulated as polymorphic when --type HW is used for simulation. 0.1
--master value Specify the master parameter for the beta distribution that describes the derived allele frequencies of the polymorphic sites when --type HW is used for simulation. 0.5
--beta value Specify the beta parameter for the beta distribution that describes the derived allele frequencies of the polymorphic sites when --type HW is used for simulation. 0.5
--F value Specify an inbreeding coefficient when --type HW is used for simulation. 0 (Will assume no inbreeding)
--seqType paired or single Specify the type or sequencing: paired-end or single-end. ‘single’
--seqCycles value Specify the number of sequencing cycles. 100
--fragmentLength 'model(parameters)' Specify model for fragment length distribution. ‘gamma(10,0.2)[30,200]’
--baseQuality 'model(parameters)' Specify model for base quality distribution. ‘normal(30,10)[0,93]’
--mappingQuality 'model(parameters)' Specify model for mapping quality distribution. ‘normal(60,10)[1,255]’
--softClipping 'model(parameters)' Specify model for soft clipping distribution. ‘poisson(0.5)[0,20]’
--pmd 'model(parameters)' Specify postmortem damage model. no pmd
--recal 'model(parameters)' Specify base quality score recalibration model. no recal
--frequency value Specify read group frequency. 1
--writeTrueGenotypes to write genotype of the simulated data do not write
--writeVariantBED to create BED file for the simulated data do not write

--seqType,--seqCycles,--fragmentLength, --baseQuality,--mappingQuality',--softClipping,--pmd,--recal can also be provided together in a separate file, Readgroupinfo.txt using the following parameter: --RGInfo Readgroupinfo.txt. See here for such an example.

Note :The number of chromosomes implied by chrLength, ploidy and depth need to match for the simulation to run! If only one value is given for --chrlength all the simulated chromosomes (implied by number of values for depth and ploidy) will have the same chromosome length.

8.2.1.3 Engine

8.2.2 Output

*.bam A Simulated bam file.
*.bam.bai Index file for the simulated bam file.
*.fasta A simulated reference sequence file.
*.fasta.fai Index file for the simulated reference sequence file.
*_trueGenotypes.vcf.gz (optional) vcf file with genotypes of the simulated data. By default genotypes are not written to a file
*_invariantSites.bed.gz (optional) BED file with invariant site positions and genotypes. By default BED files with invariant positions are not created.

8.2.3 Usage Example

# Simulate first BAM File
atlas simulate --out first

# Simulate three BAM Files using fasta-file of first bam file
atlas simulate --fasta first.fasta --sampleSize 3 --out multi