Calculate genotype posterior probabilities given family and/or known population genotypes
The tool calculates the posterior genotype probability for each sample genotype in a given VCF format callset. The input variants must present genotype likelihoods generated by HaplotypeCaller, UnifiedGenotyper or other source that provides unbiased genotype likelihoods.
The tool can use priors from three different data sources: (i) one or more supporting germline population callsets with specific annotation(s) if supplied , (ii) the pedigree for a trio if supplied and if the trio is represented in the callset under refinement, and/or (iii) the allele counts of the callset samples themselves given at least ten samples. It is possible to deactivate the contribution of the callset samples with the --ignore-input-samples flag.
For more background information and for mathematical details, see GATK forum article at https://software.broadinstitute.org/gatk/documentation/article?id=11074. Additional GATK mathematical notes are presented as whitepapers in the gatk GitHub repository docs section at https://github.com/broadinstitute/gatk/tree/master/docs.
Optionally, a collection of VCFs can be provided for the purpose of informing population allele frequency priors. Each of these resource VCFs must satisfy at least one of the following requirement sets:
A new VCF with the following information:
By default, priors will be applied to each variant separately, provided each variant features data from at least 10 called samples (no-calls do not count). SNP sites in the input callset that have a SNP at the matching site in the supporting VCF will have priors applied based on the AC from the supporting samples and the input callset unless the --ignore-input-samples flag is used. If a site is not called in the supporting VCF, priors will be applied using the discovered AC from the input samples unless the --discovered-allele-count-priors-off flag is used. For any non-SNP sites in the input callset, flat priors are applied.
For versions of the tool 4.0.5.0+, the tool appropriately applies priors to indels.
If applying family priors, only diploid family genotypes are supported. In addition, family priors only apply to trios represented in both a supplied pedigree and in the callset under refinement. Note, if the pedigree is incomplete, the tools skips calculating family priors. In this case, and in the absence of other refinement, the results will be identical to the input.
gatk --java-options "-Xmx4g" CalculateGenotypePosteriors \ -V multisample_input.vcf.gz \ -O output.vcf.gz
gatk --java-options "-Xmx4g" CalculateGenotypePosteriors \ -V sample_input.vcf.gz \ -O sample_output.1000G_PPs.vcf.gz \ -supporting 1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf.gz
gatk --java-options "-Xmx4g" CalculateGenotypePosteriors \ -V input.vcf.gz \ -O output.vcf.gz \ -ped family.ped \ --skip-population-priors
gatk --java-options "-Xmx4g" CalculateGenotypePosteriors \ -V input.vcf.gz \ -O output.vcf.gz \ --ignore-input-samples
gatk --java-options "-Xmx4g" CalculateGenotypePosteriors \ -V input.vcf.gz \ -O output.vcf.gz \ -supporting 1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf.gz \ --num-reference-samples-if-no-call 2504
If applying family priors, only diploid family genotypes are supported
This Read Filter is automatically applied to the data by the Engine before processing by CalculateGenotypePosteriors.
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Arguments | |||
| --output -O |
null | File to which variants should be written | |
| --variant -V |
null | A VCF file containing variants | |
| Optional Tool Arguments | |||
| --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). | |
| --de-novo-prior |
1.0E-6 | Prior for de novo mutations | |
| --default-to-allele-count |
false | Use AC rather than MLEAC | |
| --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! | |
| --discovered-allele-count-priors-off |
false | Do not use discovered allele count in the input callset for variants that do not appear in the external callset. | |
| --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. | |
| --global-prior-indel |
0.001 | Global Dirichlet prior parameters for the indel allele frequency | |
| --global-prior-snp |
0.001 | Global Dirichlet prior parameters for the SNP allele frequency | |
| --help -h |
false | display the help message | |
| --ignore-input-samples |
false | Use external information only | |
| --interval-merging-rule -imr |
ALL | Interval merging rule for abutting intervals | |
| --intervals -L |
[] | One or more genomic intervals over which to operate | |
| --num-reference-samples-if-no-call |
0 | Number of hom-ref genotypes to infer at sites not present in a panel | |
| --pedigree -ped |
null | Pedigree file for samples | |
| --reference -R |
null | Reference sequence | |
| --sites-only-vcf-output |
false | If true, don't emit genotype fields when writing vcf file output. | |
| --skip-family-priors |
false | Skip application of family-based priors | |
| --skip-population-priors |
false | Skip application of population-based priors | |
| --supporting-callsets -supporting |
[] | Other callsets to use in generating genotype posteriors | |
| --use-flat-priors-for-indels -skipIndels |
false | Use flat priors for indels | |
| --version |
false | display the version number for this tool | |
| Optional Common Arguments | |||
| --add-output-sam-program-record |
true | If true, adds a PG tag to created SAM/BAM/CRAM files. | |
| --add-output-vcf-command-line |
true | If true, adds a command line header line to created VCF files. | |
| --create-output-bam-index -OBI |
true | If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. | |
| --create-output-bam-md5 -OBM |
false | If true, create a MD5 digest for any BAM/SAM/CRAM file created | |
| --create-output-variant-index -OVI |
true | If true, create a VCF index when writing a coordinate-sorted VCF file. | |
| --create-output-variant-md5 -OVM |
false | If true, create a a MD5 digest any VCF file created. | |
| --disable-read-filter -DF |
[] | Read filters to be disabled before analysis | |
| --disable-tool-default-read-filters |
false | Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on) | |
| --exclude-intervals -XL |
[] | One or more genomic intervals to exclude from processing | |
| --gatk-config-file |
null | A configuration file to use with the GATK. | |
| --input -I |
[] | BAM/SAM/CRAM file containing reads | |
| --interval-exclusion-padding -ixp |
0 | Amount of padding (in bp) to add to each interval you are excluding. | |
| --interval-padding -ip |
0 | Amount of padding (in bp) to add to each interval you are including. | |
| --interval-set-rule -isr |
UNION | Set merging approach to use for combining interval inputs | |
| --lenient -LE |
false | Lenient processing of VCF files | |
| --QUIET |
false | Whether to suppress job-summary info on System.err. | |
| --read-filter -RF |
[] | Read filters to be applied before analysis | |
| --read-index |
[] | Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically. | |
| --read-validation-stringency -VS |
SILENT | Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. | |
| --seconds-between-progress-updates |
10.0 | Output traversal statistics every time this many seconds elapse | |
| --sequence-dictionary |
null | Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file. | |
| --tmp-dir |
null | 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 | |||
| --showHidden |
false | display hidden arguments | |
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
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
Prior for de novo mutations
The de novo mutation prior -- i.e. the probability that a new mutation occurs. Sensitivity analysis on known de novo
mutations suggests a default value of 10^-6.
double 1.0E-6 [ [ -∞ ∞ ] ]
Use AC rather than MLEAC
By default the tool looks for MLEAC first, and then falls back to AC if MLEAC is not found. When this
flag is set, the behavior is flipped and the tool looks first for the AC field and then fall back to MLEAC or
raw genotypes.
boolean 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.
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 read filters (WARNING: many tools will not function correctly without their default read filters on)
boolean false
Do not use discovered allele count in the input callset for variants that do not appear in the external callset.
Don't add input sample ACs for variants not seen in the supporting panel. Default is to add discovered AC from input samples
provided there are at least 10 input samples or if num-ref-samples-if-no-call is greater than zero.
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).
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.
String ""
Global Dirichlet prior parameters for the indel allele frequency
Prior indel pseudocounts for Dirichlet distribution of allele frequencies. The posterior distribution is a
Dirichlet with parameters given by pseudocounts plus the number of occurrences in the resource vcfs.
double 0.001 [ [ -∞ ∞ ] ]
Global Dirichlet prior parameters for the SNP allele frequency
Prior SNP pseudocounts for Dirichlet distribution of allele frequencies. The posterior distribution is a
Dirichlet with parameters given by pseudocounts plus the number of occurrences in the resource vcfs.
double 0.001 [ [ -∞ ∞ ] ]
display the help message
boolean false
Use external information only
When this flag is set, only the AC and AN calculated from external sources will be used, and the calculation
will not use the discovered allele frequency in the callset whose posteriors are being calculated. Useful for
callsets containing related individuals.
boolean false
BAM/SAM/CRAM file containing reads
List[String] []
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] []
Lenient processing of VCF files
boolean false
Number of hom-ref genotypes to infer at sites not present in a panel
When a variant is not seen in a 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", where AN=2*nSamples for human autosomes.
int 0 [ [ -∞ ∞ ] ]
File to which variants should be written
R File null
Pedigree file for samples
See https://software.broadinstitute.org/gatk/documentation/article.php?id=7696 for more details on the PED
format. Note that each -ped argument can be tagged with NO_FAMILY_ID, NO_PARENTS, NO_SEX, NO_PHENOTYPE to
tell the GATK PED parser that the corresponding fields are missing from the ped file.
File 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[String] []
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
String null
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.
String null
display hidden arguments
boolean false
If true, don't emit genotype fields when writing vcf file output.
boolean false
Skip application of family-based priors
Skip application of family-based priors. Note: if pedigree file is absent, family-based priors will always be skipped.
boolean false
Skip application of population-based priors
Skip application of population-based priors
boolean false
Other callsets to use in generating genotype posteriors
Supporting external panels. Allele counts from these panels (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.
List[FeatureInput[VariantContext]] []
Temp directory to use.
GATKPathSpecifier null
Use flat priors for indels
Use flat priors for indels (can be used to replicate the legacy CalculateGenotypePosteriors behavior)
If an input variant contains an indel allele, flat priors will be applied to that site. If a reference panel
variant contains an indel allele, flat priors will be applied instead.
boolean false
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
A VCF file containing variants
R String 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 4.1.4.0 built at Wed, 9 Oct 2019 15:19:59 -0400.