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 HaplotypeCaller

This 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 \
   --tmp-dir /path/to/large/tmp
 

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.
• The amount of temporary disk storage required by GenomicsDBImport may exceed what is available in the default location: `/tmp`. The command line argument `--tmp-dir` can be used to specify an alternate temperary storage location with sufficient space.

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.

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Additional Information

Read filters

This Read Filter is automatically applied to the data by the Engine before processing by GenotypeGVCFs.

• WellformedReadFilter

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		File to which variants should be written
--reference  -R		Reference sequence file
--variant  -V		A VCF file containing variants
Optional Tool Arguments
--allele-fraction-error	0.001	Margin of error in allele fraction to consider a somatic variant homoplasmic
--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
--call-genotypes	false	Output called genotypes in final VCF (otherwise no-call)
--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		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!
--flow-order-for-annotations		flow order used for this annotations. [readGroup:]flowOrder
--force-output-intervals		sites at which to output genotypes even if non-variant in samples
--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
--gcs-project-for-requester-pays		Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.
--genomicsdb-max-alternate-alleles	50	Maximum number of alternate alleles that will be combined on reading from GenomicsDB
--genomicsdb-shared-posixfs-optimizations	false	Allow for optimizations to improve the usability and performance for shared Posix Filesystems(e.g. NFS, Lustre). If set, file level locking is disabled and file system writes are minimized.
--genomicsdb-use-gcs-hdfs-connector	false	Use the GCS HDFS Connector instead of the native GCS SDK client with gs:// URLs.
--genotype-assignment-method  -gam	USE_PLS_TO_ASSIGN	How we assign genotypes
--help  -h	false	display the help message
--heterozygosity	0.001	Heterozygosity value used to compute prior probabilities 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.
--include-non-variant-sites  -all-sites	false	Include loci found to be non-variant after genotyping
--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
--input-is-somatic	false	Finalize input GVCF according to somatic (i.e. Mutect2) TLODs (BETA feature)
--interval-merging-rule  -imr	ALL	Interval merging rule for abutting intervals
--intervals  -L		One or more genomic intervals over which to operate
--keep-combined-raw-annotations  -keep-combined	false	If specified, keep the combined raw annotations
--merge-input-intervals	false	Boolean flag to import all data in between intervals.
--num-reference-samples-if-no-call	0	Number of hom-ref genotypes to infer at sites not present in a panel
--pedigree  -ped		Pedigree file for determining the population "founders"
--population-callset  -population		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	30.0	The minimum phred-scaled confidence threshold at which variants should be called
--tumor-lod-to-emit  -emit-lod	3.5	LOD threshold to emit variant to VCF.
--use-posteriors-to-calculate-qual  -gp-qual	false	if available, use the genotype posterior probabilities to calculate the site QUAL
--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		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
--max-variants-per-shard	0	If non-zero, partitions VCF output into shards, each containing up to the given number of records.
--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		Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
--tmp-dir		Temp directory to use.
--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
--dont-use-dragstr-priors	false	Forfeit the use of the DRAGstr model to calculate genotype priors. This argument does not have any effect in the absence of DRAGstr model parameters (--dragstr-model-params)
--enable-all-annotations	false	Use all possible annotations (not for the faint of heart)
--genomicsdb-use-bcf-codec	false	Use BCF Codec Streaming for data from GenomicsDB instead of the default VCFCodec. BCFCodec performs slightly better but currently does not support 64-bit width positions and INFO fields and for computed annotation sizes to exceed 32-bit integer space.
--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
Deprecated Arguments
--use-new-qual-calculator  -new-qual	true	Use the new AF model instead of the so-called exact model

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

---

--allele-fraction-error

Margin of error in allele fraction to consider a somatic variant homoplasmic
Margin of error in allele fraction to consider a somatic variant homoplasmic, i.e. if there is less than a 0.1% reference allele fraction, those reads are likely errors

double  0.001  [ [ -∞  ∞ ] ]

---

--annotate-with-num-discovered-alleles

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]  []

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--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

read one or more arguments files and add them to the command line

List[File]  []

---

--call-genotypes

Output called genotypes in final VCF (otherwise no-call)
Output called genotypes in the final VCF (otherwise no-call)

boolean  false

---

--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

---

--dont-use-dragstr-priors

Forfeit the use of the DRAGstr model to calculate genotype priors. This argument does not have any effect in the absence of DRAGstr model parameters (--dragstr-model-params)

boolean  false

---

--enable-all-annotations

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]  []

---

--flow-order-for-annotations

flow order used for this annotations. [readGroup:]flowOrder

List[String]  []

---

--force-output-intervals

sites at which to output genotypes even if non-variant in samples

List[String]  []

---

--founder-id / -founder-id

Samples representing the population "founders"

List[String]  []

---

--gatk-config-file

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  [ [ -∞  ∞ ] ]

---

--gcs-project-for-requester-pays

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.

String  ""

---

--genomicsdb-max-alternate-alleles

Maximum number of alternate alleles that will be combined on reading from GenomicsDB
Maximum number of alternate alleles that will report likelihoods after being combined on reading from GenomicsDB (including ) Must be at least one greater than the maximum number of alternate alleles for genotyping. A typical value is 3 more than the --max-alternate-alleles value that's used by GenotypeGVCFs and larger differences result in more robustness to PCR-related indel errors. NOTE: GenotypeGVCFs will drop multi-allelic sites with more than this many alternate alleles since they are missing likelihoods. See also {@link org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection#MAX_ALTERNATE_ALLELES_LONG_NAME}

int  50  [ [ -∞  ∞ ] ]

---

--genomicsdb-shared-posixfs-optimizations

Allow for optimizations to improve the usability and performance for shared Posix Filesystems(e.g. NFS, Lustre). If set, file level locking is disabled and file system writes are minimized.

boolean  false

---

--genomicsdb-use-bcf-codec

Use BCF Codec Streaming for data from GenomicsDB instead of the default VCFCodec. BCFCodec performs slightly better but currently does not support 64-bit width positions and INFO fields and for computed annotation sizes to exceed 32-bit integer space.
Currently there is no support for 64-bit fields in BCF2Codec. The VCFCodec allows for 64-bit width positions and INFO fields and for computed annotation sizes to exceed the 32-bit integer space while encoding/decoding with GenomicsDB. Use the BCF2Codec option if and only if performance is an issue.

boolean  false

---

--genomicsdb-use-gcs-hdfs-connector

Use the GCS HDFS Connector instead of the native GCS SDK client with gs:// URLs.

boolean  false

---

--genotype-assignment-method / -gam

How we assign genotypes

The --genotype-assignment-method argument is an enumerated type (GenotypeAssignmentMethod), which can have one of the following values:

SET_TO_NO_CALL

set all of the genotype GT values to NO_CALL

USE_PLS_TO_ASSIGN

Use the subsetted PLs to greedily assign genotypes

USE_POSTERIORS_ANNOTATION

Use the existing, subsetted posteriors array to assign genotypes

SET_TO_NO_CALL_NO_ANNOTATIONS

set all of the genotype GT values to NO_CALL and remove annotations

BEST_MATCH_TO_ORIGINAL

Try to match the original GT calls, if at all possible Suppose I have 3 alleles: A/B/C and the following samples: original_GT best_match to A/B best_match to A/C S1 => A/A A/A A/A S2 => A/B A/B A/A S3 => B/B B/B A/A S4 => B/C A/B A/C S5 => C/C A/A C/C Basically, all alleles not in the subset map to ref. It means that het-alt genotypes when split into 2 bi-allelic variants will be het in each, which is good in some cases, rather than the undetermined behavior when using the PLs to assign, which could result in hom-var or hom-ref for each, depending on the exact PL values.

DO_NOT_ASSIGN_GENOTYPES

do not even bother changing the GTs

USE_POSTERIOR_PROBABILITIES

Calculate posterior probabilities and use those to assign genotypes

PREFER_PLS

Use PLs unless they are unavailable, in which case use best match to original

GenotypeAssignmentMethod  USE_PLS_TO_ASSIGN

---

--help / -h

display the help message

boolean  false

---

--heterozygosity

Heterozygosity value used to compute prior probabilities 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

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  [ [ -∞  ∞ ] ]

---

--include-non-variant-sites / -all-sites

Include loci found to be non-variant after genotyping

boolean  false

---

--indel-heterozygosity

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[GATKPath]  []

---

--input-is-somatic

Finalize input GVCF according to somatic (i.e. Mutect2) TLODs (BETA feature)
"Genotype" somatic GVCFs, outputting genotypes according to confidently called alt alleles, which may lead to inconsistent ploidy Note that the Mutect2 reference confidence mode is in BETA -- the likelihoods model and output format are subject to change in subsequent versions.

boolean  false

---

--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]  []

---

--keep-combined-raw-annotations / -keep-combined

If specified, keep the combined raw annotations
If specified, keep the combined raw annotations (e.g. AS_SB_TABLE) after genotyping. This is applicable to Allele-Specific annotations

boolean  false

---

--lenient / -LE

Lenient processing of VCF files

boolean  false

---

--max-alternate-alleles

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 #maxGenotypeCount} and {@link org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection#MAX_ALTS_LONG_NAME}. This value can be no greater than one less than the corresponding GenomicsDB argument. Sites that exceed the GenomicsDB alt allele max will not be output with likelihoods and will be dropped by GenotypeGVCFs.

int  6  [ [ -∞  ∞ ] ]

---

--max-genotype-count

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 assumption. 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 #maxGenotypeCount} 2. the value of {@link #maxAlternateAlleles} See also {@link #maxAlternateAlleles} and {@link org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection#maxDiploidAltAllelesThatCanBeGenotyped}

int  1024  [ [ -∞  ∞ ] ]

---

--max-variants-per-shard

If non-zero, partitions VCF output into shards, each containing up to the given number of records.

int  0  [ [ 0  ∞ ] ]

---

--merge-input-intervals / -merge-input-intervals

Boolean flag to import all data in between intervals.
Import all data between specified intervals. Improves performance using large lists of intervals, as in exome sequencing, especially if GVCF data only exists for specified intervals. Use with --only-output-calls-starting-in-intervals if input GVCFs contain calls outside the specified intervals.

boolean  false

---

--num-reference-samples-if-no-call

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

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 GATKPath  null

---

--pedigree / -ped

Pedigree file for determining the population "founders"

GATKPath  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

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[GATKPath]  []

---

--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 GATKPath  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 chromoso mes 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.

GATKPath  null

---

--showHidden / -showHidden

display hidden arguments

boolean  false

---

--sites-only-vcf-output

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. Note that the default was changed from 10.0 to 30.0 in version 4.1.0.0 to accompany the switch to use the the new quality score by default.

double  30.0  [ [ -∞  ∞ ] ]

---

--tmp-dir

Temp directory to use.

GATKPath  null

---

--tumor-lod-to-emit / -emit-lod

LOD threshold to emit variant to VCF.
Only variants with tumor LODs exceeding this threshold will be written to the VCF, regardless of filter status. Set to less than or equal to tumor_lod. Increase argument value to reduce false positives in the callset.

double  3.5  [ [ -∞  ∞ ] ]

---

--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

Use the new AF model instead of the so-called exact model
As of version 4.1.0.0, this argument is no longer needed because the new qual score is now on by default. See GATK 3.3 release notes for more details.

boolean  true

---

--use-posteriors-to-calculate-qual / -gp-qual

if available, use the genotype posterior probabilities to calculate the site QUAL

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

display the version number for this tool

boolean  false

---

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GATK version 4.3.0.0 built at Wed, 12 Oct 2022 21:04:44 -0400.