Condenses homRef blocks in a single-sample GVCF

Category Other

---

Overview

Condense 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. 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.

Input

A HaplotypeCaller-produced GVCF to reblock

Output

A smaller GVCF.

Usage example

 gatk ReblockGVCF \
   -R reference.fasta \
   -V sample1.g.vcf \
   -O sample1.reblocked.g.vcf
 

Invocation as for use with GnarlyGenotyper in the "Biggest Practices"

  gatk ReblockGVCF \
    -R reference.fasta \
    -V sample1.g.vcf \
    -drop-low-quals \
    -rgq-threshold 10 \
    -do-qual-approx \
    -O sample1.reblocked.g.vcf
  * 

Caveats

Only single-sample GVCF files produced by HaplotypeCaller can be used as input for this tool.

Special note on ploidy

This tool assumes diploid genotypes.

---

Additional Information

Read filters

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

• WellformedReadFilter

ReblockGVCF 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
--variant  -V		A VCF file containing variants
Optional Tool Arguments
--annotate-with-num-discovered-alleles	false	If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site
--annotation  -A		One or more specific annotations to add to variant calls
--annotation-group  -G		One or more groups of annotations to apply to variant calls
--annotations-to-exclude  -AX		One or more specific annotations to exclude from variant calls
--arguments_file		read one or more arguments files and add them to the command line
--cloud-index-prefetch-buffer  -CIPB	-1	Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
--cloud-prefetch-buffer  -CPB	40	Size of the cloud-only prefetch buffer (in MB; 0 to disable).
--dbsnp  -D		dbSNP file
--disable-bam-index-caching  -DBIC	false	If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.
--disable-sequence-dictionary-validation	false	If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
--founder-id		Samples representing the population "founders"
--gcs-max-retries  -gcs-retries	20	If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--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 likelihoods for any locus. See the GATKDocs for full details on the meaning of this population genetics concept
--heterozygosity-stdev	0.01	Standard deviation of heterozygosity for SNP and indel calling.
--indel-heterozygosity	1.25E-4	Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept
--interval-merging-rule  -imr	ALL	Interval merging rule for abutting intervals
--intervals  -L		One or more genomic intervals over which to operate
--num-reference-samples-if-no-call	0	Number of hom-ref genotypes to infer at sites not present in a panel
--pedigree  -ped		Pedigree file for determining the population "founders"
--population-callset  -population		Callset to use in calculating genotype priors
--reference  -R		Reference sequence
--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-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
--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.
--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
--gvcf-gq-bands  -GQB	[20, 100]	Exclusive upper bounds for reference confidence GQ bands (must be in [1, 100] and specified in increasing order)
--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
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

---

--allow-missing-hom-ref-data

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

---

--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]  []

---

--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]  []

---

--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

---

--do-qual-score-approximation / -do-qual-approx

Add necessary INFO field annotation to perform QUAL approximation downstream; required for GnarlyGenotyper

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

---

--drop-low-quals / -drop-low-quals

Exclude variants and homRef blocks that are GQ0 from the reblocked GVCF to save space; drop low quality/uncalled alleles

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]  []

---

--floor-blocks

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

boolean  false

---

--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  ""

---

--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 assigned 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

Use posterior probabilities:

GenotypeAssignmentMethod  USE_PLS_TO_ASSIGN

---

--gvcf-gq-bands / -GQB

Exclusive upper bounds for reference confidence GQ bands (must be in [1, 100] and specified in increasing order)

List[Integer]  [20, 100]

---

--help / -h

display the help message

boolean  false

---

--heterozygosity

Heterozygosity value used to compute prior likelihoods for any locus. See the GATKDocs for full details on the meaning of this population genetics concept
The expected heterozygosity value used to compute prior probability that a locus is non-reference. The default priors are for provided for humans: het = 1e-3 which means that the probability of N samples being hom-ref at a site is: 1 - sum_i_2N (het / i) Note that heterozygosity as used here is the population genetics concept: http://en.wikipedia.org/wiki/Zygosity#Heterozygosity_in_population_genetics That is, a hets value of 0.01 implies that two randomly chosen chromosomes from the population of organisms would differ from each other (one being A and the other B) at a rate of 1 in 100 bp. Note that this quantity has nothing to do with the likelihood of any given sample having a heterozygous genotype, which in the GATK is purely determined by the probability of the observed data P(D | AB) under the model that there may be a AB het genotype. The posterior probability of this AB genotype would use the het prior, but the GATK only uses this posterior probability in determining the prob. that a site is polymorphic. So changing the het parameters only increases the chance that a site will be called non-reference across all samples, but doesn't actually change the output genotype likelihoods at all, as these aren't posterior probabilities at all. The quantity that changes whether the GATK considers the possibility of a het genotype at all is the ploidy, which determines how many chromosomes each individual in the species carries.

Double  0.001  [ [ -∞  ∞ ] ]

---

--heterozygosity-stdev

Standard deviation of heterozygosity for SNP and indel calling.
The standard deviation of the distribution of alt allele fractions. The above heterozygosity parameters give the *mean* of this distribution; this parameter gives its spread.

double  0.01  [ [ -∞  ∞ ] ]

---

--indel-heterozygosity

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]  []

---

--interval-exclusion-padding / -ixp

Amount of padding (in bp) to add to each interval you are excluding.
Use this to add padding to the intervals specified using -XL. For example, '-XL 1:100' with a padding value of 20 would turn into '-XL 1:80-120'. This is typically used to add padding around targets when analyzing exomes.

int  0  [ [ -∞  ∞ ] ]

---

--interval-merging-rule / -imr

Interval merging rule for abutting intervals
By default, the program merges abutting intervals (i.e. intervals that are directly side-by-side but do not actually overlap) into a single continuous interval. However you can change this behavior if you want them to be treated as separate intervals instead.

The --interval-merging-rule argument is an enumerated type (IntervalMergingRule), which can have one of the following values:

ALL

OVERLAPPING_ONLY

IntervalMergingRule  ALL

---

--interval-padding / -ip

Amount of padding (in bp) to add to each interval you are including.
Use this to add padding to the intervals specified using -L. For example, '-L 1:100' with a padding value of 20 would turn into '-L 1:80-120'. This is typically used to add padding around targets when analyzing exomes.

int  0  [ [ -∞  ∞ ] ]

---

--interval-set-rule / -isr

Set merging approach to use for combining interval inputs
By default, the program will take the UNION of all intervals specified using -L and/or -XL. However, you can change this setting for -L, for example if you want to take the INTERSECTION of the sets instead. E.g. to perform the analysis only on chromosome 1 exomes, you could specify -L exomes.intervals -L 1 --interval-set-rule INTERSECTION. However, it is not possible to modify the merging approach for intervals passed using -XL (they will always be merged using UNION). Note that if you specify both -L and -XL, the -XL interval set will be subtracted from the -L interval set.

The --interval-set-rule argument is an enumerated type (IntervalSetRule), which can have one of the following values:

UNION

Take the union of all intervals

INTERSECTION

Take the intersection of intervals (the subset that overlaps all intervals specified)

IntervalSetRule  UNION

---

--intervals / -L

One or more genomic intervals over which to operate

List[String]  []

---

--lenient / -LE

Lenient processing of VCF files

boolean  false

---

--max-alternate-alleles

Maximum number of alternate alleles to genotype
If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES), then only this many alleles will be used. Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it scales exponentially based on the number of alternate alleles. Unless there is a good reason to change the default value, we highly recommend that you not play around with this parameter. See also {@link #MAX_GENOTYPE_COUNT}.

int  6  [ [ -∞  ∞ ] ]

---

--max-genotype-count

Maximum number of genotypes to consider at any site
If there are more than this number of genotypes at a locus presented to the genotyper, then only this many genotypes will be used. The possible genotypes are simply different ways of partitioning alleles given a specific ploidy asumption. Therefore, we remove genotypes from consideration by removing alternate alleles that are the least well supported. The estimate of allele support is based on the ranking of the candidate haplotypes coming out of the graph building step. Note that the reference allele is always kept. Note that genotyping sites with large genotype counts is both CPU and memory intensive. Unless there is a good reason to change the default value, we highly recommend that you not play around with this parameter. The maximum number of alternative alleles used in the genotyping step will be the lesser of the two: 1. the largest number of alt alleles, given ploidy, that yields a genotype count no higher than {@link #MAX_GENOTYPE_COUNT} 2. the value of {@link #MAX_ALTERNATE_ALLELES} See also {@link #MAX_ALTERNATE_ALLELES}.

int  1024  [ [ -∞  ∞ ] ]

---

--max-variants-per-shard

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

int  0  [ [ 0  ∞ ] ]

---

--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  [ [ -∞  ∞ ] ]

---

--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

GATKPath  null

---

--rgq-threshold-to-no-call / -rgq-threshold

Reference genotype quality (PL[0]) value below which variant sites will be converted to GQ0 homRef calls

double  0.0  [ [ -∞  ∞ ] ]

---

--sample-ploidy / -ploidy

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

int  2  [ [ -∞  ∞ ] ]

---

--seconds-between-progress-updates / -seconds-between-progress-updates

Output traversal statistics every time this many seconds elapse

double  10.0  [ [ -∞  ∞ ] ]

---

--sequence-dictionary / -sequence-dictionary

Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.

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

---

--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 GATKPath  null

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--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

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--version

display the version number for this tool

boolean  false

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GATK version 4.2.1.0-1-gf548ccd-SNAPSHOT built at Mon, 2 Aug 2021 14:22:45 -0700.