Perform joint genotyping on one or more samples pre-called with HaplotypeCaller
Category Short Variant Discovery
Overview
Perform joint genotyping on one or more samples pre-called with HaplotypeCallerThis tool is designed to perform joint genotyping on a single input, which may contain one or many samples. In any case, the input samples must possess genotype likelihoods produced by HaplotypeCaller with `-ERC GVCF` or `-ERC BP_RESOLUTION`.
Input
The GATK4 GenotypeGVCFs tool can take only one input track. Options are 1) a single single-sample GVCF 2) a single multi-sample GVCF created by CombineGVCFs or 3) a GenomicsDB workspace created by GenomicsDBImport. A sample-level GVCF is produced by HaplotypeCaller with the `-ERC GVCF` setting.
Output
A final VCF in which all samples have been jointly genotyped.
Usage example
Perform joint genotyping on a singular sample by providing a single-sample GVCF or on a cohort by providing a combined multi-sample GVCF
gatk --java-options "-Xmx4g" GenotypeGVCFs \ -R Homo_sapiens_assembly38.fasta \ -V input.g.vcf.gz \ -O output.vcf.gz
Perform joint genotyping on GenomicsDB workspace created with GenomicsDBImport
gatk --java-options "-Xmx4g" GenotypeGVCFs \ -R Homo_sapiens_assembly38.fasta \ -V gendb://my_database \ -O output.vcf.gz
Caveats
- 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.
- Cannot take multiple GVCF files in one command.
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.
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 Arguments | |||
| --output -O |
null | File to which variants should be written | |
| --reference -R |
null | Reference sequence file | |
| --variant -V |
null | A VCF file containing variants | |
| Optional Tool Arguments | |||
| --annotate-with-num-discovered-alleles |
false | If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site | |
| --annotation -A |
[] | One or more specific annotations to add to variant calls | |
| --annotation-group -G |
[] | One or more groups of annotations to apply to variant calls | |
| --annotations-to-exclude -AX |
[] | One or more specific annotations to exclude from variant calls | |
| --arguments_file |
[] | read one or more arguments files and add them to the command line | |
| --cloud-index-prefetch-buffer -CIPB |
-1 | Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset. | |
| --cloud-prefetch-buffer -CPB |
40 | Size of the cloud-only prefetch buffer (in MB; 0 to disable). | |
| --dbsnp -D |
null | dbSNP file | |
| --disable-bam-index-caching -DBIC |
false | If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified. | |
| --disable-sequence-dictionary-validation |
false | If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk! | |
| --founder-id |
[] | Samples representing the population "founders" | |
| --gcs-max-retries -gcs-retries |
20 | If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection | |
| --help -h |
false | display the help message | |
| --heterozygosity |
0.001 | Heterozygosity value used to compute prior likelihoods for any locus. See the GATKDocs for full details on the meaning of this population genetics concept | |
| --heterozygosity-stdev |
0.01 | Standard deviation of heterozygosity for SNP and indel calling. | |
| --indel-heterozygosity |
1.25E-4 | Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept | |
| --interval-merging-rule -imr |
ALL | Interval merging rule for abutting intervals | |
| --intervals -L |
[] | One or more genomic intervals over which to operate | |
| --num-reference-samples-if-no-call |
0 | Number of hom-ref genotypes to infer at sites not present in a panel | |
| --pedigree -ped |
null | Pedigree file for determining the population "founders" | |
| --population-callset -population |
null | Callset to use in calculating genotype priors | |
| --sample-ploidy -ploidy |
2 | Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy). | |
| --sites-only-vcf-output |
false | If true, don't emit genotype fields when writing vcf file output. | |
| --standard-min-confidence-threshold-for-calling -stand-call-conf |
10.0 | The minimum phred-scaled confidence threshold at which variants should be called | |
| --use-new-qual-calculator -new-qual |
false | If provided, we will use the new AF model instead of the so-called exact model | |
| --version |
false | display the version number for this tool | |
| Optional Common Arguments | |||
| --add-output-sam-program-record |
true | If true, adds a PG tag to created SAM/BAM/CRAM files. | |
| --add-output-vcf-command-line |
true | If true, adds a command line header line to created VCF files. | |
| --create-output-bam-index -OBI |
true | If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. | |
| --create-output-bam-md5 -OBM |
false | If true, create a MD5 digest for any BAM/SAM/CRAM file created | |
| --create-output-variant-index -OVI |
true | If true, create a VCF index when writing a coordinate-sorted VCF file. | |
| --create-output-variant-md5 -OVM |
false | If true, create a a MD5 digest any VCF file created. | |
| --disable-read-filter -DF |
[] | Read filters to be disabled before analysis | |
| --disable-tool-default-read-filters |
false | Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on) | |
| --exclude-intervals -XL |
[] | One or more genomic intervals to exclude from processing | |
| --gatk-config-file |
null | A configuration file to use with the GATK. | |
| --input -I |
[] | BAM/SAM/CRAM file containing reads | |
| --interval-exclusion-padding -ixp |
0 | Amount of padding (in bp) to add to each interval you are excluding. | |
| --interval-padding -ip |
0 | Amount of padding (in bp) to add to each interval you are including. | |
| --interval-set-rule -isr |
UNION | Set merging approach to use for combining interval inputs | |
| --lenient -LE |
false | Lenient processing of VCF files | |
| --QUIET |
false | Whether to suppress job-summary info on System.err. | |
| --read-filter -RF |
[] | Read filters to be applied before analysis | |
| --read-index |
[] | Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically. | |
| --read-validation-stringency -VS |
SILENT | Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. | |
| --seconds-between-progress-updates |
10.0 | Output traversal statistics every time this many seconds elapse | |
| --sequence-dictionary |
null | Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file. | |
| --TMP_DIR |
[] | Undocumented option | |
| --use-jdk-deflater -jdk-deflater |
false | Whether to use the JdkDeflater (as opposed to IntelDeflater) | |
| --use-jdk-inflater -jdk-inflater |
false | Whether to use the JdkInflater (as opposed to IntelInflater) | |
| --verbosity |
INFO | Control verbosity of logging. | |
| Advanced Arguments | |||
| --disable-tool-default-annotations |
false | Disable all tool default annotations | |
| --enable-all-annotations |
false | Use all possible annotations (not for the faint of heart) | |
| --input-prior |
[] | Input prior for calls | |
| --max-alternate-alleles |
6 | Maximum number of alternate alleles to genotype | |
| --max-genotype-count |
1024 | Maximum number of genotypes to consider at any site | |
| --only-output-calls-starting-in-intervals |
false | Restrict variant output to sites that start within provided intervals | |
| --showHidden |
false | display hidden arguments | |
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.
--add-output-sam-program-record / -add-output-sam-program-record
If true, adds a PG tag to created SAM/BAM/CRAM files.
boolean true
--add-output-vcf-command-line / -add-output-vcf-command-line
If true, adds a command line header line to created VCF files.
boolean true
--annotate-with-num-discovered-alleles / NA
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 add to variant calls
Which annotations to include in variant calls in the output. These supplement annotations provided by annotation groups.
List[String] []
--annotation-group / -G
One or more groups of annotations to apply to variant calls
Which groups of annotations to add to the output variant calls.
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] []
--annotations-to-exclude / -AX
One or more specific annotations to exclude from variant calls
Which annotations to exclude from output in the variant calls. Note that this argument has higher priority than the
-A or -G arguments, so these annotations will be excluded even if they are explicitly included with the other
options.
List[String] []
--arguments_file / NA
read one or more arguments files and add them to the command line
List[File] []
--cloud-index-prefetch-buffer / -CIPB
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
int -1 [ [ -∞ ∞ ] ]
--cloud-prefetch-buffer / -CPB
Size of the cloud-only prefetch buffer (in MB; 0 to disable).
int 40 [ [ -∞ ∞ ] ]
--create-output-bam-index / -OBI
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
boolean true
--create-output-bam-md5 / -OBM
If true, create a MD5 digest for any BAM/SAM/CRAM file created
boolean false
--create-output-variant-index / -OVI
If true, create a VCF index when writing a coordinate-sorted VCF file.
boolean true
--create-output-variant-md5 / -OVM
If true, create a a MD5 digest any VCF file created.
boolean false
--dbsnp / -D
dbSNP file
A dbSNP VCF file.
FeatureInput[VariantContext] null
--disable-bam-index-caching / -DBIC
If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.
boolean false
--disable-read-filter / -DF
Read filters to be disabled before analysis
List[String] []
--disable-sequence-dictionary-validation / -disable-sequence-dictionary-validation
If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
boolean false
--disable-tool-default-annotations / -disable-tool-default-annotations
Disable all tool default annotations
Hook allowing for the user to remove default annotations from the tool
boolean false
--disable-tool-default-read-filters / -disable-tool-default-read-filters
Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
boolean false
--enable-all-annotations / NA
Use all possible annotations (not for the faint of heart)
You can use the -AX argument in combination with this one to exclude specific annotations. Note that some
annotations may not be actually applied if they are not applicable to the data provided or if they are
unavailable to the tool (e.g. there are several annotations that are currently not hooked up to
HaplotypeCaller). At present no error or warning message will be provided, the annotation will simply be
skipped silently. You can check the output VCF header to see which annotations were activated and thus might be applied (although
this does not guarantee that the annotation was applied to all records in the VCF, since some annotations have
additional requirements, e.g. minimum number of samples or heterozygous sites only -- see the documentation
for individual annotations' requirements).
boolean false
--exclude-intervals / -XL
One or more genomic intervals to exclude from processing
Use this argument to exclude certain parts of the genome from the analysis (like -L, but the opposite).
This argument can be specified multiple times. You can use samtools-style intervals either explicitly on the
command line (e.g. -XL 1 or -XL 1:100-200) or by loading in a file containing a list of intervals
(e.g. -XL myFile.intervals).
List[String] []
--founder-id / -founder-id
Samples representing the population "founders"
List[String] []
--gatk-config-file / NA
A configuration file to use with the GATK.
String null
--gcs-max-retries / -gcs-retries
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
--help / -h
display the help message
boolean false
--heterozygosity / NA
Heterozygosity value used to compute prior likelihoods for any locus. See the GATKDocs for full details on the meaning of this population genetics concept
The expected heterozygosity value used to compute prior probability that a locus is non-reference.
The default priors are for provided for humans:
het = 1e-3
which means that the probability of N samples being hom-ref at a site is:
1 - sum_i_2N (het / i)
Note that heterozygosity as used here is the population genetics concept:
http://en.wikipedia.org/wiki/Zygosity#Heterozygosity_in_population_genetics
That is, a hets value of 0.01 implies that two randomly chosen chromosomes from the population of organisms
would differ from each other (one being A and the other B) at a rate of 1 in 100 bp.
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 [ [ -∞ ∞ ] ]
--heterozygosity-stdev / NA
Standard deviation of heterozygosity for SNP and indel calling.
The standard deviation of the distribution of alt allele fractions. The above heterozygosity parameters give the
*mean* of this distribution; this parameter gives its spread.
double 0.01 [ [ -∞ ∞ ] ]
--indel-heterozygosity / NA
Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept
This argument informs the prior probability of having an indel at a site.
double 1.25E-4 [ [ -∞ ∞ ] ]
--input / -I
BAM/SAM/CRAM file containing reads
List[String] []
--input-prior / NA
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 desireable, 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, user can manually specify priors to be used for calling as a vector for doubles, with the following restriciotns:
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.
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] []
--interval-exclusion-padding / -ixp
Amount of padding (in bp) to add to each interval you are excluding.
Use this to add padding to the intervals specified using -XL. For example, '-XL 1:100' with a
padding value of 20 would turn into '-XL 1:80-120'. This is typically used to add padding around targets when
analyzing exomes.
int 0 [ [ -∞ ∞ ] ]
--interval-merging-rule / -imr
Interval merging rule for abutting intervals
By default, the program merges abutting intervals (i.e. intervals that are directly side-by-side but do not
actually overlap) into a single continuous interval. However you can change this behavior if you want them to be
treated as separate intervals instead.
The --interval-merging-rule argument is an enumerated type (IntervalMergingRule), which can have one of the following values:
- ALL
- OVERLAPPING_ONLY
IntervalMergingRule ALL
--interval-padding / -ip
Amount of padding (in bp) to add to each interval you are including.
Use this to add padding to the intervals specified using -L. For example, '-L 1:100' with a
padding value of 20 would turn into '-L 1:80-120'. This is typically used to add padding around targets when
analyzing exomes.
int 0 [ [ -∞ ∞ ] ]
--interval-set-rule / -isr
Set merging approach to use for combining interval inputs
By default, the program will take the UNION of all intervals specified using -L and/or -XL. However, you can
change this setting for -L, for example if you want to take the INTERSECTION of the sets instead. E.g. to
perform the analysis only on chromosome 1 exomes, you could specify -L exomes.intervals -L 1 --interval-set-rule
INTERSECTION. However, it is not possible to modify the merging approach for intervals passed using -XL (they will
always be merged using UNION).
Note that if you specify both -L and -XL, the -XL interval set will be subtracted from the -L interval set.
The --interval-set-rule argument is an enumerated type (IntervalSetRule), which can have one of the following values:
- UNION
- Take the union of all intervals
- INTERSECTION
- Take the intersection of intervals (the subset that overlaps all intervals specified)
IntervalSetRule UNION
--intervals / -L
One or more genomic intervals over which to operate
List[String] []
--lenient / -LE
Lenient processing of VCF files
boolean false
--max-alternate-alleles / NA
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.
See also {@link #MAX_GENOTYPE_COUNT}.
int 6 [ [ -∞ ∞ ] ]
--max-genotype-count / NA
Maximum number of genotypes to consider at any site
If there are more than this number of genotypes at a locus presented to the genotyper, then only this many genotypes will be used.
The possible genotypes are simply different ways of partitioning alleles given a specific ploidy asumption.
Therefore, we remove genotypes from consideration by removing alternate alleles that are the least well supported.
The estimate of allele support is based on the ranking of the candidate haplotypes coming out of the graph building step.
Note that the reference allele is always kept.
Note that genotyping sites with large genotype counts is both CPU and memory intensive.
Unless there is a good reason to change the default value, we highly recommend that you not play around with this parameter.
The maximum number of alternative alleles used in the genotyping step will be the lesser of the two:
1. the largest number of alt alleles, given ploidy, that yields a genotype count no higher than {@link #MAX_GENOTYPE_COUNT}
2. the value of {@link #MAX_ALTERNATE_ALLELES}
See also {@link #MAX_ALTERNATE_ALLELES}.
int 1024 [ [ -∞ ∞ ] ]
--num-reference-samples-if-no-call / NA
Number of hom-ref genotypes to infer at sites not present in a panel
When a variant is not seen in any panel, this argument controls whether to infer (and with what effective strength)
that only reference alleles were observed at that site. E.g. "If not seen in 1000Genomes, treat it as AC=0,
AN=2000".
int 0 [ [ -∞ ∞ ] ]
--only-output-calls-starting-in-intervals / NA
Restrict variant output to sites that start within provided intervals
This option can only be activated if intervals are specified.
boolean false
--output / -O
File to which variants should be written
R File null
--pedigree / -ped
Pedigree file for determining the population "founders"
File null
--population-callset / -population
Callset to use in calculating genotype priors
Supporting external panel. Allele counts from this panel (taken from AC,AN or MLEAC,AN or raw genotypes) will
be used to inform the frequency distribution underlying the genotype priors. These files must be VCF 4.2 spec or later.
Note that unlike CalculateGenotypePosteriors, HaplotypeCaller only allows one supporting callset.
FeatureInput[VariantContext] null
--QUIET / NA
Whether to suppress job-summary info on System.err.
Boolean false
--read-filter / -RF
Read filters to be applied before analysis
List[String] []
--read-index / -read-index
Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.
List[String] []
--read-validation-stringency / -VS
Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
The --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:
- STRICT
- LENIENT
- SILENT
ValidationStringency SILENT
--reference / -R
Reference sequence file
R String null
--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 [ [ -∞ ∞ ] ]
--seconds-between-progress-updates / -seconds-between-progress-updates
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
--sequence-dictionary / -sequence-dictionary
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
String null
--showHidden / -showHidden
display hidden arguments
boolean false
--sites-only-vcf-output / NA
If true, don't emit genotype fields when writing vcf file output.
boolean false
--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 confidence threshold at which variants should be called. Only variant sites with QUAL equal
or greater than this threshold will be called. Note that since version 3.7, we no longer differentiate high confidence
from low confidence calls at the calling step. The default call confidence threshold is set low intentionally to achieve
high sensitivity, which will allow false positive calls as a side effect. Be sure to perform some kind of filtering after
calling to reduce the amount of false positives in your final callset. Note that when HaplotypeCaller is used in GVCF mode
(using either -ERC GVCF or -ERC BP_RESOLUTION) the call threshold is automatically set to zero. Call confidence thresholding
will then be performed in the subsequent GenotypeGVCFs command.
double 10.0 [ [ -∞ ∞ ] ]
--TMP_DIR / NA
Undocumented option
List[File] []
--use-jdk-deflater / -jdk-deflater
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
--use-jdk-inflater / -jdk-inflater
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
--use-new-qual-calculator / -new-qual
If provided, we will use the new AF model instead of the so-called exact model
Use the new allele frequency / QUAL score model
boolean false
--variant / -V
A VCF file containing variants
R String null
--verbosity / -verbosity
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
- ERROR
- WARNING
- INFO
- DEBUG
LogLevel INFO
--version / NA
display the version number for this tool
boolean false
GATK version 4.0.5.0 built at 25-10-2019 02:10:54.
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