Condenses homRef blocks in a single-sample GVCF
ReblockGVCF compresses a GVCF by merging hom-ref blocks that were produced using the '-ERC GVCF' or '-ERC BP_RESOLUTION' mode of the HaplotypeCaller according to new GQ band parameters. Uncalled alleles and associated data will also be dropped unless --keep-all-alts is specified. A joint callset produced with GVCFs reprocessed by ReblockGVCF will have lower precision for hom-ref genotype qualities at variant sites, but the input data footprint can be greatly reduced if the default GQ band parameters are used.
A HaplotypeCaller-produced GVCF to reblock
A smaller GVCF.
gatk ReblockGVCF \ -GQB 20 -GQB 30 -GQB 40 --floor-blocks \ -R reference.fasta \ -V sample1.g.vcf \ -O sample1.rb.g.vcfInvocation as for smallest GVCFs to use with GnarlyGenotyper
gatk ReblockGVCF \
-R reference.fasta \
-V sample1.g.vcf \
-drop-low-quals \
-rgq-threshold 10 \
-do-qual-approx \
-O sample1.reblocked.g.vcf
*
Only single-sample GVCF files produced by HaplotypeCaller can be used as input for this tool.
Annotations and header lines that are uninformative for single-sample will be dropped: MLEAC, MLEAF, DS, ExcessHet, HaplotypeScore, InbreedingCoeff, AS_InbreedingCoeff
Note that when uncalled alleles are dropped, the original GQ may increase. Use --keep-all-alts if GQ accuracy is a concern.
This Read Filter is automatically applied to the data by the Engine before processing by ReblockGVCF.
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 |
One or more VCF files 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 |
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 | ||
| --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. | ||
| --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. | |
| --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 |
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 | |
| --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 | |||
| --add-site-filters-to-genotype |
false | Add site level filters to genotype level. Site level filters removed by default, if they should be kept, use --keep-site-filters | |
| --allow-missing-hom-ref-data |
false | Fill in homozygous reference genotypes with no PLs and no GQ with PL=[0,0,0]. Necessary for input from Regeneron's WeCall variant caller. | |
| --annotations-to-keep |
Annotations that are not recognized by GATK to keep, that should be kept in final GVCF at variant sites. | ||
| --disable-tool-default-annotations |
false | Disable all tool default annotations | |
| --do-qual-score-approximation -do-qual-approx |
false | Add necessary INFO field annotation to perform QUAL approximation downstream; required for GnarlyGenotyper | |
| --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) | |
| --drop-low-quals |
false | Exclude variants and homRef blocks that are GQ0 from the reblocked GVCF to save space; drop low quality/uncalled alleles | |
| --enable-all-annotations |
false | Use all possible annotations (not for the faint of heart) | |
| --floor-blocks |
false | Output the band lower bound for each GQ block regardless of the data it represents | |
| --format-annotations-to-remove |
FORMAT level annotations to remove from all genotypes in final GVCF. | ||
| --gvcf-gq-bands -GQB |
[20, 100] | Exclusive upper bounds for reference confidence GQ bands (must be in [1, 100] and specified in increasing order) | |
| --keep-all-alts |
false | Keep all ALT alleles and full PL array for most accurate GQs | |
| --keep-site-filters -keep-filters |
false | Keep site level filters for variants (not ref blocks). | |
| --max-alternate-alleles |
6 | Maximum number of alternate alleles to genotype | |
| --max-genotype-count |
1024 | Maximum number of genotypes to consider at any site | |
| --rgq-threshold-to-no-call -rgq-threshold |
0.0 | Reference genotype quality (PL[0]) value below which variant sites will be converted to GQ0 homRef calls | |
| --showHidden |
false | display hidden arguments | |
| --tree-score-threshold-to-no-call |
0.0 | Tree score value below which variant sites will be converted to GQ0 homRef calls. Disabled when set to 0 (which is the default). | |
| --variant-output-filtering |
Restrict the output variants to ones that match the specified intervals according to the specified matching mode. | ||
| Deprecated Arguments | |||
| --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
Add site level filters to genotype level. Site level filters removed by default, if they should be kept, use --keep-site-filters
boolean false
Fill in homozygous reference genotypes with no PLs and no GQ with PL=[0,0,0]. Necessary for input from Regeneron's WeCall variant caller.
boolean false
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] []
Annotations that are not recognized by GATK to keep, that should be kept in final GVCF at variant sites.
List[String] []
read one or more arguments files and add them to the command line
List[File] []
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 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
Add necessary INFO field annotation to perform QUAL approximation downstream; required for GnarlyGenotyper
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
Exclude variants and homRef blocks that are GQ0 from the reblocked GVCF to save space; drop low quality/uncalled alleles
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] []
Output the band lower bound for each GQ block regardless of the data it represents
Output the band lower bound for each GQ block instead of the min GQ -- for better compression
Note that this argument also drops PLS for more efficient storage
boolean false
flow order used for this annotations. [readGroup:]flowOrder
List[String] []
FORMAT level annotations to remove from all genotypes in final GVCF.
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 ""
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
Exclusive upper bounds for reference confidence GQ bands (must be in [1, 100] and specified in increasing order)
List[Integer] [20, 100]
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 [ [ -∞ ∞ ] ]
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] []
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] []
Keep all ALT alleles and full PL array for most accurate GQs
boolean false
Keep site level filters for variants (not ref blocks).
boolean false
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 ∞ ] ]
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 [ [ -∞ ∞ ] ]
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
Reference genotype quality (PL[0]) value below which variant sites will be converted to GQ0 homRef calls
double 0.0 [ [ -∞ ∞ ] ]
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
Tree score value below which variant sites will be converted to GQ0 homRef calls. Disabled when set to 0 (which is the default).
double 0.0 [ [ -∞ ∞ ] ]
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
One or more VCF files containing variants
R List[GATKPath] []
Restrict the output variants to ones that match the specified intervals according to the specified matching mode.
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.