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# Simulate Genomic Variants

Simulate snps, indels, inversions, cnv, translocations

  • a reference genome in FASTA format: .fasta .fa .fasta.gz .fa.gz case insensitive

You may want to benchmark haplotag data on different kinds of genomic variants. To do that, you'll need known variants, and typically simulations are how you achieve that. This series of modules simulates genomic variants onto a genome, either randomly or specific variants provided in VCF files. The simulator Harpy uses, simuG, can only simulate one type of variant at a time and each variant type has their own set of parameters. This page is divided by variant types to help you navigate the process. The general usage for simulating variants is:

usage
harpy simulate variant OPTIONS... INPUT_GENOME
example
harpy simulate inversion -n 10 --min-size 1000 --max-size 50000  path/to/genome.fasta

# Modules

There are 4 submodules with very obvious names:

submodule what it does
snpindel simulates single nucleotide polymorphisms (snps) and insertion-deletions (indels)
inversion simulates inversions
cnv simulates copy number variants
translocation simulates translocations

# Running Options

While there are serveral differences between individual workflow options, each has available all the common runtime options like other Harpy modules. Each requires and input genome at the end of the command line, and each requires either a --count of variants to randomly simulate, or a --vcf of specific variants to simulate. There are also these unifying options among the different variant types:

argument short name description
INPUT_GENOME required The haploid genome to simulate variants onto
--centromeres -c GFF3 file of centromeres to avoid
--exclude-chr -e Text file of chromosomes to avoid, one per line
--genes -g GFF3 file of genes to avoid simulating over (see snpindel for caveat)
--heterozygosity -z proportion of simulated variants to make heterozygous (default: 0)
--only-vcf When used with --heterozygosity, will create the diploid VCFs but will not simulate a diploid genome
--prefix Naming prefix for output files (default: sim.{module_name})
--randomseed Random seed for simulation

# snpindel

A single nucleotide polymorphism ("SNP") is a genomic variant at a single base position in the DNA (source). An indel, is a type of mutation that involves the addition/deletion of one or more nucleotides into a segment of DNA (insertions, deletions). The snp and indel variants are combined in this module because simuG allows simulating them together.

argument short name default description
--indel-count -m 0 Number of random indels to simluate
--indel-vcf -i VCF file of known indels to simulate
--indel-ratio -d 1 Insertion/Deletion ratio for indels
--indel-size-alpha -a 2.0 Exponent Alpha for power-law-fitted indel size distribution
--indel-size-constant -l 0.5 Exponent constant for power-law-fitted indel size distribution
--snp-count -n 0 Number of random snps to simluate
--snp-gene-constraints -y How to constrain randomly simulated SNPs {noncoding,coding,2d,4d} when using --genes
--snp-vcf -s VCF file of known snps to simulate
--titv-ratio -r 0.5 Transition/Transversion ratio for snps

The ratio parameters for snp and indel variants and have special meanings when setting the value to either 0 or 9999 :

ratio 0 meaning 9999 meaning
--indel-ratio deletions only insertions only
--titv-ratio transversions only transitions only

# inversion

Inversions are when a section of a chromosome appears in the reverse orientation (source).

argument short name default description
--count -n 0 Number of random inversions to simluate
--max-size -x 100000 Maximum inversion size (bp)
--min-size -m 1000 Minimum inversion size (bp)
--vcf -v VCF file of known inversions to simulate

# cnv

A copy number variation (CNV) is when the number of copies of a particular gene varies between individuals (source).

argument short name default description
--vcf -v VCF file of known copy number variants to simulate
--count -n 0 Number of random cnv to simluate
--dup-ratio -d 1 Tandem/Dispersed duplication ratio
--gain-ratio -l 1 Relative ratio of DNA gain over DNA loss
--max-size -x 100000 Maximum cnv size (bp)
--max-copy -y 10 Maximum number of copies
--min-size -m 1000 Minimum cnv size (bp)

The ratio parameters have special meanings when setting the value to either 0 or 9999 :

ratio 0 meaning 9999 meaning
--dup-ratio dispersed duplications only tandem duplications only
--gain-ratio loss only gain only

# translocation

A translocation occurs when a chromosome breaks and the fragmented pieces re-attach to different chromosomes (source).

argument short name default description
--count -n 0 Number of random inversions to simluate
--vcf -v VCF file of known inversions to simulate

# Simulate known variants

Rather than simulating random variants, you can use a VCF file as input to any of the workflows to have simuG simulate the variants (of that type) from the VCF file. This becomes particularly handy because the modules output a VCF file of the variants that were introduced, which you can modify and reuse as you see fit (see heterozygosity). Using --genes, --centromeres, or --exclude-chr would still avoid creating variants in those regions as with random simulation, except with SNPs, where you would have to specify the contraints for using --genes as per usual.

# Heterozygosity

Each workflow has a --heterozygosity parameter where you can specify the heterozygosity of the simulated variants, which creates two new VCF files ({prefix}.hap1.vcf, {prefix}.hap2.vcf) that have their variants shuffled between the two haplotypes to achieve the desired heterozygosity. The workflows will then use the new "diploid" variants to generate a diploid genome-- one fasta file for each haplotype. You can disable the creation of the diploid fasta files using --only-vcf, which will still create the VCF files of the variants to your chosen heterozygosity.

To understand how heterozygosity is created from the simuG VCF output, consider a genome with 5 variants added to it, here represented as a column labelled h1 with 1 being the presence of a variant (the ALT allele).

h1
1
1
1
1
1

If we were to simulate those same variants onto the genome again, it would create a homozygote at every position (h2 is the second haplotype):

h1 h2
1  1
1  1
1  1
1  1
1  1

However, if we omit some of the variants on h2 to create 40% heterozygosity (2/5), we would now have heterozygotes, except the ALT allele for the heterozygote would only every be on the first haplotype h1:

h1 h2
1  1
1  1
1  1
1     <- heterozygote with ALT on h1
1     <- heterozygote with ALT on h1

It would probably be more biologically sound to then make sure that the ALT allele in the heterozygote can appear in either haplotype:

h1 h2
1  1
1  1
1  1
   1  <- heterozygote with ALT on h2
1     <- heterozygote with ALT on h1

Within Harpy, a heterozygous variant has a 50% chance of being assigned to one of the haplotypes. So that's the logic behind the --heterozygosity parameter and why it ouputs 3 VCF files:

  1. the VCF simuG outputs of variants added to the genome
  2. haplotype 1 of that VCF file with some of the variants
  3. haplotype 2 of that VCF file with some of the variants

Knowing that, you can then have a workflow to start with a haploid assembly and create a diploid assembly with simulated variants.

# Variant Simulation Workflow 

graph LR
   geno[input genome]:::clean
   simhap([simulate haploid variants]):::clean
   makedipl([create diploids]):::clean
   simhap1([simulate haplotype 1]):::clean
   simhap2([simulate haplotype 2]):::clean
   haplo1([haplotype1.fasta])
   haplo2([haplotype2.fasta])
   geno--->simhap
   simhap--->|--heterozygosity > 0|makedipl
   makedipl--->simhap1
   makedipl--->simhap2
   simhap1--->haplo1
   simhap2--->haplo2
   subgraph diploid ["diploid variants"]
        haplo1
        haplo2
    end
   classDef clean fill:#f5f6f9,stroke:#b7c9ef,stroke-width:2px
   style diploid fill:#f0f0f0,stroke:#e8e8e8,stroke-width:2px
   style haplo1 stroke:#90c8be,fill:#f0f0f0,stroke-width:2px
   style haplo2 stroke:#bd8fcb,fill:#f0f0f0,stroke-width:2px

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