## Overview

Given a set of variants, this tool will generate simulated reads that support the input variants.

### Caveats

For practical reasons, only bi-allelic variants that are not too close to the ends of contigs (< 1/2 read length) are supported; all others will simply be ignored.

### Input

A VCF file containing variants.

### Output

A BAM file containing simulated sequence reads that support the input variants, with the requested error rate and coverage depth.

### Example

 java -Xmx2g -jar GenomeAnalysisTK.jar \
-R reference.fasta \
-V input_variants.vcf \
--errorRate 25


These Read Filters are automatically applied to the data by the Engine before processing by SimulateReadsForVariants.

### Downsampling settings

This tool applies the following downsampling settings by default.

• Mode: BY_SAMPLE
• To coverage: 1,000

### Window size

This tool uses a sliding window on the reference.

• Window start: -200 bp before the locus
• Window stop: 200 bp after the locus

## Command-line Arguments

### Inherited arguments

The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Required Inputs
--variant
-V
NA Input VCF file
Required Outputs
--out
-o
Optional Parameters
--errorRate
-ER
20 Base error rate (Phred-scaled)
-DP
-RL
-RSM
CONSTANT Sampling mode
--rgPlatform
-RGPL
ILLUMINA Sequencing platform

### Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

### --errorRate / -ER

Base error rate (Phred-scaled)
Errors will be generated at this rate in the simulated reads. Base qualities are therefore also assigned this value.

int  20  [ [ 0  2,147,483,647 ] ]

### --out / -o

The simulated reads will be written to a BAM file.

R GATKSAMFileWriter

Use this argument to set the desired target read depth. See the readSamplingMode argument for options that determine whether coverage distribution will be exactly this value or an approximation.

int  20  [ [ 0  [ 1  1,000 ]  2,147,483,647 ] ]

All simulated reads will be exactly this length.

int  101  [ [ 1  2,147,483,647 ] ]

Sampling mode
This determines how read sampling is achieved, and affects the coverage distribution of simulated reads. CONSTANT sampling will produce uniform depth at all positions, while POISSON sampling will produce a distribution of coverages around the requested value.

The --readSamplingMode argument is an enumerated type (ReadSamplingMode), which can have one of the following values:

CONSTANT
POISSON

### --rgPlatform / -RGPL

Sequencing platform
The corresponding platform identifier will be specified in the simulated read group PL tag. This setting does not affect the properties of the simulated reads.

The --rgPlatform argument is an enumerated type (NGSPlatform), which can have one of the following values:

ILLUMINA
SOLID
LS454
COMPLETE_GENOMICS
PACBIO
ION_TORRENT
CAPILLARY
HELICOS
UNKNOWN

NGSPlatform  ILLUMINA

### --variant / -V

Input VCF file
Variants from this VCF file are used by this tool as input. The file must at least contain the standard VCF header lines, but can be empty (i.e., no variants are contained in the file).

--variant binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3

R RodBinding[VariantContext]

GATK version 3.2-2-gec30cee built at 2014/09/12 22:29:29. GTD: EB