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SimulateReadsForVariants

Generate simulated reads for variants

Category Diagnostics and Quality Control Tools

Traversal LocusWalker

PartitionBy LOCUS


Overview

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

Caveat

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.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T SimulateReadsForVariants \
   -R reference.fasta \
   -V input_variants.vcf \
   -o simulated_reads.bam \
   --readDepth 50 \
   --errorRate 25
 

Additional Information

Read filters

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

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

Engine arguments

All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.

SimulateReadsForVariants specific arguments

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
NA Reads corresponding to variants
Optional Parameters
--errorRate
 -ER
20 Base error rate (Phred-scaled)
--readDepth
 -DP
20 Read depth to generate
--readLength
 -RL
101 Read lengths (bp)
Advanced Parameters
--readSamplingMode
 -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

Reads corresponding to variants
The simulated reads will be written to a BAM file.

R GATKSAMFileWriter  NA


--readDepth / -DP

Read depth to generate
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 ] ]


--readLength / -RL

Read lengths (bp)
All simulated reads will be exactly this length.

int  101  [ [ 1  2,147,483,647 ] ]


--readSamplingMode / -RSM

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

ReadSamplingMode  CONSTANT


--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).

This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3

R RodBinding[VariantContext]  NA


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GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.