Showing docs for version 3.6-0 | The latest version is 4.1.4.0


GenotypeGVCFs

Perform joint genotyping on gVCF files produced by HaplotypeCaller

Category Variant Discovery Tools

Traversal LocusWalker

PartitionBy LOCUS


Overview

GenotypeGVCFs merges gVCF records that were produced as part of the Best Practices workflow for variant discovery (see Best Practices documentation for more details) using the '-ERC GVCF' or '-ERC BP_RESOLUTION' mode of the HaplotypeCaller, or result from combining such gVCF files using CombineGVCFs. This tool performs the multi-sample joint aggregation step and merges the records together in a sophisticated manner: at each position of the input gVCFs, this tool will combine all spanning records, produce correct genotype likelihoods, re-genotype the newly merged record, and then re-annotate it.

Input

One or more HaplotypeCaller gVCFs to genotype.

Output

A combined, genotyped VCF.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T GenotypeGVCFs \
   -R reference.fasta \
   --variant sample1.g.vcf \
   --variant sample2.g.vcf \
   -o output.vcf
 

Caveat

Only gVCF files produced by HaplotypeCaller (or CombineGVCFs) can be used as input for this tool. Some other programs produce files that they call gVCFs but those lack some important information (accurate genotype likelihoods for every position) that GenotypeGVCFs requires for its operation.

Special note on ploidy

This tool is able to handle any ploidy (or mix of ploidies) intelligently; there is no need to specify ploidy for non-diploid organisms.


Additional Information

Read filters

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

Parallelism options

This tool can be run in multi-threaded mode using this option.

Window size

This tool uses a sliding window on the reference.

  • Window start: -10 bp before the locus
  • Window stop: 10 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.

GenotypeGVCFs 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 One or more input gVCF files
Optional Inputs
--dbsnp
 -D
none dbSNP file
Optional Outputs
--out
 -o
stdout File to which variants should be written
Optional Parameters
--group
 -G
[StandardAnnotation] One or more classes/groups of annotations to apply to variant calls
--heterozygosity
 -hets
0.001 Heterozygosity value used to compute prior likelihoods for any locus
--indel_heterozygosity
 -indelHeterozygosity
1.25E-4 Heterozygosity for indel calling
--sample_ploidy
 -ploidy
2 Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).
--standard_min_confidence_threshold_for_calling
 -stand_call_conf
30.0 The minimum phred-scaled confidence threshold at which variants should be called
--standard_min_confidence_threshold_for_emitting
 -stand_emit_conf
30.0 The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)
Optional Flags
--annotateNDA
 -nda
false If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site
--includeNonVariantSites
 -allSites
false Include loci found to be non-variant after genotyping
Advanced Parameters
--annotation
 -A
[] One or more specific annotations to recompute. The single value 'none' removes the default annotations
--input_prior
 -inputPrior
[] Input prior for calls
--max_alternate_alleles
 -maxAltAlleles
6 Maximum number of alternate alleles to genotype
--max_num_PL_values
 -maxNumPLValues
100 Maximum number of PL values to output

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.


--annotateNDA / -nda

If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site
Depending on the value of the --max_alternate_alleles argument, we may genotype only a fraction of the alleles being sent on for genotyping. Using this argument instructs the genotyper to annotate (in the INFO field) the number of alternate alleles that were originally discovered at the site.

boolean  false


--annotation / -A

One or more specific annotations to recompute. The single value 'none' removes the default annotations
Which annotations to recompute for the combined output VCF file.

List[String]  []


--dbsnp / -D

dbSNP file
The rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate. Note that dbSNP is not used in any way for the calculations themselves.

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

RodBinding[VariantContext]  none


--group / -G

One or more classes/groups of annotations to apply to variant calls
Which groups of annotations to add to the output VCF file. The single value 'none' removes the default group. See the VariantAnnotator -list argument to view available groups. Note that this usage is not recommended because it obscures the specific requirements of individual annotations. Any requirements that are not met (e.g. failing to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.

List[String]  [StandardAnnotation]


--heterozygosity / -hets

Heterozygosity value used to compute prior likelihoods for any locus
The expected heterozygosity value used to compute prior probability that a locus is non-reference. From the heterozygosity we calculate the probability of N samples being hom-ref at a site as 1 - sum_i_2N (hets / i) where hets is this case is analogous to the parameter theta from population genetics. See https://en.wikipedia.org/wiki/Coalescent_theory for more details. Note that heterozygosity as used here is the population genetics concept. (See http://en.wikipedia.org/wiki/Zygosity#Heterozygosity_in_population_genetics. We also suggest the book "Population Genetics: A Concise Guide" by John H. Gillespie for further details on the theory.) That is, a hets value of 0.001 implies that two randomly chosen chromosomes from the population of organisms would differ from each other at a rate of 1 in 1000 bp. The default priors provided for humans (hets = 1e-3) Also note that this quantity has nothing to do with the likelihood of any given sample having a heterozygous genotype, which in the GATK is purely determined by the probability of the observed data P(D | AB) under the model that there may be a AB het genotype. The posterior probability of this AB genotype would use the het prior, but the GATK only uses this posterior probability in determining the prob. that a site is polymorphic. So changing the het parameters only increases the chance that a site will be called non-reference across all samples, but doesn't actually change the output genotype likelihoods at all, as these aren't posterior probabilities at all. The quantity that changes whether the GATK considers the possibility of a het genotype at all is the ploidy, which determines how many chromosomes each individual in the species carries.

Double  0.001  [ [ -∞  ∞ ] ]


--includeNonVariantSites / -allSites

Include loci found to be non-variant after genotyping

boolean  false


--indel_heterozygosity / -indelHeterozygosity

Heterozygosity for indel calling
This argument informs the prior probability of having an indel at a site.

double  1.25E-4  [ [ -∞  ∞ ] ]


--input_prior / -inputPrior

Input prior for calls
By default, the prior specified with the argument --heterozygosity/-hets is used for variant discovery at a particular locus, using an infinite sites model, see e.g. Waterson (1975) or Tajima (1996). This model asserts that the probability of having a population of k variant sites in N chromosomes is proportional to theta/k, for 1=1:N There are instances where using this prior might not be desirable, e.g. for population studies where prior might not be appropriate, as for example when the ancestral status of the reference allele is not known. By using this argument, the user can manually specify a list of probabilities for each AC>1 to be used as priors for genotyping, with the following restrictions: a) User must specify 2N values, where N is the number of samples. b) Only diploid calls supported. c) Probability values are specified in Double format, in linear space (not log10 space or Phred-scale). d) No negative values allowed. e) Values will be added and Pr(AC=0) will be 1-sum, so that they sum up to one. f) If user-defined values add to more than one, an error will be produced. If user wants completely flat priors, then user should specify the same value (=1/(2*N+1)) 2*N times,e.g. -inputPrior 0.33 -inputPrior 0.33 for the single-sample diploid case.

List[Double]  []


--max_alternate_alleles / -maxAltAlleles

Maximum number of alternate alleles to genotype
If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN_ALLELES), then only this many alleles will be used. Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it scales exponentially based on the number of alternate alleles. Unless there is a good reason to change the default value, we highly recommend that you not play around with this parameter. As of GATK 2.2 the genotyper can handle a very large number of events, so the default maximum has been increased to 6.

int  6  [ [ -∞  ∞ ] ]


--max_num_PL_values / -maxNumPLValues

Maximum number of PL values to output
Determines the maximum number of PL values that will be logged in the output. If the number of genotypes (which is determined by the ploidy and the number of alleles) exceeds the value provided by this argument, then output of all of the PL values will be suppressed.

int  100  [ [ -∞  ∞ ] ]


--out / -o

File to which variants should be written

VariantContextWriter  stdout


--sample_ploidy / -ploidy

Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).
Sample ploidy - equivalent to number of chromosomes per pool. In pooled experiments this should be = # of samples in pool * individual sample ploidy

int  2  [ [ -∞  ∞ ] ]


--standard_min_confidence_threshold_for_calling / -stand_call_conf

The minimum phred-scaled confidence threshold at which variants should be called
The minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls. Only genotypes with confidence >= this threshold are emitted as called sites. A reasonable threshold is 30 for high-pass calling (this is the default).

double  30.0  [ [ -∞  ∞ ] ]


--standard_min_confidence_threshold_for_emitting / -stand_emit_conf

The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)
This argument allows you to emit low quality calls as filtered records.

double  30.0  [ [ -∞  ∞ ] ]


--variant / -V

One or more input gVCF files
The gVCF files to merge together

R List[RodBindingCollection[VariantContext]]  NA


Return to top


See also GATK Documentation Index | Tool Docs Index | Support Forum

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