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`.
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.
A final VCF in which all samples have been jointly genotyped.
gatk --java-options "-Xmx4g" GenotypeGVCFs \ -R Homo_sapiens_assembly38.fasta \ -V input.g.vcf.gz \ -O output.vcf.gz
gatk --java-options "-Xmx4g" GenotypeGVCFs \ -R Homo_sapiens_assembly38.fasta \ -V gendb://my_database \ -O output.vcf.gz \ --tmp-dir /path/to/large/tmp
This tool is able to handle any ploidy (or mix of ploidies) intelligently; there is no need to specify ploidy for non-diploid organisms.
This Read Filter is automatically applied to the data by the Engine before processing by GenotypeGVCFs.
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 | |
| --keep-specific-combined-raw-annotation -keep-specific-combined |
Keep only the specific combined raw annotations specified (removing the other raw annotations). Duplicate values will be ignored. | ||
| --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-new-qual-calculator -new-qual |
true | (Deprecated) Use the new AF model instead of the so-called exact model | |
| --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 | |
| --inverted-read-filter -XRF |
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters). | ||
| --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 | (Deprecated) Restrict variant output to sites that start within provided intervals, equivalent to '--variant-output-filtering STARTS_IN' | |
| --showHidden |
false | display hidden arguments | |
| --variant-output-filtering |
Restrict the output variants to ones that match the specified intervals according to the specified matching mode. | ||
| Deprecated Arguments | |||
| --only-output-calls-starting-in-intervals |
false | (Deprecated) Restrict variant output to sites that start within provided intervals, equivalent to '--variant-output-filtering STARTS_IN' | |
| --use-new-qual-calculator -new-qual |
true | (Deprecated) Use the new AF model instead of the so-called exact model | |
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.
If true, adds a PG tag to created SAM/BAM/CRAM files.
boolean true
If true, adds a command line header line to created VCF files.
boolean true
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 [ [ -∞ ∞ ] ]
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
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] []
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] []
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] []
read one or more arguments files and add them to the command line
List[File] []
Output called genotypes in final VCF (otherwise no-call)
Output called genotypes in the final VCF (otherwise no-call)
boolean false
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
int -1 [ [ -∞ ∞ ] ]
Size of the cloud-only prefetch buffer (in MB; 0 to disable).
int 40 [ [ -∞ ∞ ] ]
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
boolean true
If true, create a MD5 digest for any BAM/SAM/CRAM file created
boolean false
If true, create a VCF index when writing a coordinate-sorted VCF file.
boolean true
If true, create a a MD5 digest any VCF file created.
boolean false
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 genotyping calculations themselves.
FeatureInput[VariantContext] null
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
Read filters to be disabled before analysis
List[String] []
If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
boolean false
Disable all tool default annotations
Hook allowing for the user to remove default annotations from the tool
boolean false
Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
boolean 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)
boolean false
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
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). strings gathered from the command line -XL argument to be parsed into intervals to exclude
List[String] []
flow order used for this annotations. [readGroup:]flowOrder
List[String] []
sites at which to output genotypes even if non-variant in samples
List[String] []
Samples representing the population "founders"
List[String] []
A configuration file to use with the GATK.
String null
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
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 ""
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
int 50 [ [ -∞ ∞ ] ]
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
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
Use the GCS HDFS Connector instead of the native GCS SDK client with gs:// URLs.
boolean false
How we assign genotypes
The --genotype-assignment-method argument is an enumerated type (GenotypeAssignmentMethod), which can have one of the following values:
GenotypeAssignmentMethod USE_PLS_TO_ASSIGN
display the help message
boolean false
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 [ [ -∞ ∞ ] ]
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 loci found to be non-variant after genotyping
boolean false
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 [ [ -∞ ∞ ] ]
BAM/SAM/CRAM file containing reads
List[GATKPath] []
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
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 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:
IntervalMergingRule ALL
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 [ [ -∞ ∞ ] ]
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:
IntervalSetRule UNION
One or more genomic intervals over which to operate
List[String] []
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters).
List[String] []
If specified, keep the combined raw annotations
If specified, keep all the combined raw annotations (e.g. AS_SB_TABLE) after genotyping. This is applicable to Allele-Specific annotations. See
Exclusion: This argument cannot be used at the same time as keep-specific-combined-raw-annotation.
boolean false
Keep only the specific combined raw annotations specified (removing the other raw annotations). Duplicate values will be ignored.
Keep only the specific combined raw annotations specified. Cannot be used with --keep-combined-raw-annotations which saves all raw annotations.
Duplicate values will be ignored. See for more information on raw annotations.
Exclusion: This argument cannot be used at the same time as keep-combined-raw-annotations.
List[String] []
Lenient processing of VCF files
boolean false
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 and .
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 [ [ -∞ ∞ ] ]
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
2. the value of
See also and
int 1024 [ [ -∞ ∞ ] ]
If non-zero, partitions VCF output into shards, each containing up to the given number of records.
int 0 [ [ 0 ∞ ] ]
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
-- if input GVCFs contain calls outside the specified intervals.
boolean false
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 [ [ -∞ ∞ ] ]
(Deprecated)
Restrict variant output to sites that start within provided intervals, equivalent to '--variant-output-filtering STARTS_IN'
This option can only be activated if intervals are specified.
Exclusion: This argument cannot be used at the same time as variant-output-filtering.
boolean false
File to which variants should be written
R GATKPath null
Pedigree file for determining the population "founders"
GATKPath null
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
Whether to suppress job-summary info on System.err.
Boolean false
Read filters to be applied before analysis
List[String] []
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] []
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:
ValidationStringency SILENT
Reference sequence file
R GATKPath null
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 [ [ -∞ ∞ ] ]
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
GATKPath null
display hidden arguments
boolean false
If true, don't emit genotype fields when writing vcf file output.
boolean false
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 [ [ -∞ ∞ ] ]
Temp directory to use.
GATKPath null
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 [ [ -∞ ∞ ] ]
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
(Deprecated)
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
if available, use the genotype posterior probabilities to calculate the site QUAL
boolean false
A VCF file containing variants
R String null
Restrict the output variants to ones that match the specified intervals according to the specified matching mode.
Exclusion: This argument cannot be used at the same time as only-output-calls-starting-in-intervals.
The --variant-output-filtering argument is an enumerated type (Mode), which can have one of the following values:
Mode null
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
LogLevel INFO
display the version number for this tool
boolean false
See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum
GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.