General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)
Given a variant callset, it is common to calculate various quality control metrics. These metrics include the number of raw or filtered SNP counts; ratio of transition mutations to transversions; concordance of a particular sample's calls to a genotyping chip; number of s per sample; etc. Furthermore, it is often useful to stratify these metrics by various criteria like functional class (missense, nonsense, silent), whether the site is CpG site, the amino acid degeneracy of the site, etc. VariantEval facilitates these calculations in two ways: by providing several built-in evaluation and stratification modules, and by providing a framework that permits the easy development of new evaluation and stratification modules.
One or more variant sets to evaluate plus any number of comparison sets.
Evaluation tables detailing the results of the eval modules which were applied. For example:
output.eval.grp: ##:GATKReport.v0.1 CountVariants : Counts different classes of variants in the sample CountVariants CompFeatureInput CpG EvalFeatureInput JexlExpression Novelty nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate ... CountVariants dbsnp CpG eval none all 65900028 135770 0 135770 0.00206024 ... CountVariants dbsnp CpG eval none known 65900028 47068 0 47068 0.00071423 ... CountVariants dbsnp CpG eval none novel 65900028 88702 0 88702 0.00134601 ... CountVariants dbsnp all eval none all 65900028 330818 0 330818 0.00502000 ... CountVariants dbsnp all eval none known 65900028 120685 0 120685 0.00183133 ... CountVariants dbsnp all eval none novel 65900028 210133 0 210133 0.00318866 ... CountVariants dbsnp non_CpG eval none all 65900028 195048 0 195048 0.00295976 ... CountVariants dbsnp non_CpG eval none known 65900028 73617 0 73617 0.00111710 ... CountVariants dbsnp non_CpG eval none novel 65900028 121431 0 121431 0.00184265 ... ...
gatk VariantEval \ -R reference.fasta \ -O output.eval.grp \ --eval set1:set1.vcf \ --eval set2:set2.vcf \ [--comp comp.vcf]Count Mendelian violations for each family in a callset with multiple families (and provided pedigree)
gatk VariantEval \ -R reference.fasta \ -O output.MVs.byFamily.table \ --eval multiFamilyCallset.vcf \ -no-ev -noST \ -ST Family \ -EV MendelianViolationEvaluator
Some stratifications and evaluators are incompatible with each other due to their respective memory requirements, such as AlleleCount and VariantSummary, or Sample and VariantSummary. If you specify such a combination, the program will output an error message and ask you to disable one of these options. We do not currently provide an exhaustive list of incompatible combinations, so we recommend trying out combinations that you are interested in on a dummy command line, to rapidly ascertain whether it will work or not.
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 | |||
| --eval |
Input evaluation file(s) | ||
| --output -O |
File to which variants should be written | ||
| --reference -R |
Reference sequence file | ||
| Optional Tool Arguments | |||
| --ancestral-alignments -aa |
Fasta file with ancestral alleles | ||
| --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). | |
| --comparison -comp |
Input comparison file(s) | ||
| --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! | |
| --do-not-use-all-standard-modules -no-ev |
false | Do not use the standard modules by default (instead, only those that are specified with the -EV option) | |
| --do-not-use-all-standard-stratifications -no-st |
false | Do not use the standard stratification modules by default (instead, only those that are specified with the -S option) | |
| --eval-module -EV |
One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -no-ev is specified) | ||
| --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. | ||
| --gold-standard -gold |
Evaluations that count calls at sites of true variation (e.g., indel calls) will use this argument as their gold standard for comparison | ||
| --help -h |
false | display the help message | |
| --interval-merging-rule -imr |
ALL | Interval merging rule for abutting intervals | |
| --intervals -L |
One or more genomic intervals over which to operate | ||
| --keep-ac0 |
false | If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes | |
| --known-cnvs |
File containing tribble-readable features describing a known list of copy number variants | ||
| --knownNames -known-name |
Name of feature bindings containing variant sites that should be treated as known when splitting eval features into known and novel subsets | ||
| --list -ls |
false | List the available eval modules and exit | |
| --mendelian-violation-qual-threshold -mvq |
50.0 | Minimum genotype QUAL score for each trio member required to accept a site as a violation. Default is 50. | |
| --merge-evals |
false | If provided, all -eval tracks will be merged into a single eval track | |
| --min-phase-quality -mpq |
10.0 | Minimum phasing quality | |
| --pedigree -ped |
Pedigree file for determining the population "founders" | ||
| --pedigreeValidationType -pedValidationType |
STRICT | The strictness for validating the pedigree. Can be either STRICT or SILENT. Default is STRICT | |
| --require-strict-allele-match -strict |
false | If provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping | |
| --sample -sn |
Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context | ||
| --sample-ploidy -ploidy |
2 | Per-sample ploidy (number of chromosomes per sample) | |
| --selectExps -select |
One or more stratifications to use when evaluating the data | ||
| --selectNames -select-name |
Names to use for the list of stratifications (must be a 1-to-1 mapping) | ||
| --sites-only-vcf-output |
false | If true, don't emit genotype fields when writing vcf file output. | |
| --strat-intervals |
File containing tribble-readable features for the IntervalStratificiation | ||
| --stratification-module -ST |
One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified) | ||
| --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. | |
| --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-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 | |||
| --combine-variants-distance |
0 | Maximum distance for variants to be grouped together | |
| --ignore-variants-starting-outside-interval |
false | Restrict variant output to sites that start within provided intervals (only applies when an interval is specified) | |
| --max-distance |
2147483647 | Maximum distance for variants to be grouped together | |
| --ref-padding |
1 | Number of bases on either side to expand spanning reference window | |
| --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. | ||
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
Fasta file with ancestral alleles
File null
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 [ [ -∞ ∞ ] ]
Maximum distance for variants to be grouped together
int 0 [ [ -∞ ∞ ] ]
Input comparison file(s)
The variant file(s) to compare against.
List[FeatureInput[VariantContext]] []
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
A dbSNP VCF file.
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
If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
boolean false
Do not use the standard modules by default (instead, only those that are specified with the -EV option)
Boolean false
Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)
Boolean false
Input evaluation file(s)
The variant file(s) to evaluate.
R List[FeatureInput[VariantContext]] []
One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -no-ev is specified)
See the -list argument to view available modules.
List[String] []
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] []
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 ""
Evaluations that count calls at sites of true variation (e.g., indel calls) will use this argument as their gold standard for comparison
Some analyses want to count overlap not with dbSNP (which is in general very open) but
actually want to itemize their overlap specifically with a set of gold standard sites
such as HapMap, OMNI, or the gold standard indels. This argument provides a mechanism
for communicating which file to use
FeatureInput[VariantContext] null
display the help message
boolean false
Restrict variant output to sites that start within provided intervals (only applies when an interval is specified)
this option has no effect unless intervals are specified.
This exists to mimic GATK3 interval traversal patterns
boolean false
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] []
If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes
boolean false
File containing tribble-readable features describing a known list of copy number variants
File containing tribble-readable features containing known CNVs. For use with VariantSummary table.
FeatureInput[Feature] null
Name of feature bindings containing variant sites that should be treated as known when splitting eval features into known and novel subsets
List of feature tracks to be used for specifying "known" variants other than dbSNP.
Set[String] []
Lenient processing of VCF files
boolean false
List the available eval modules and exit
Note that the --list argument requires a fully resolved and correct command-line to work.
Boolean false
Maximum distance for variants to be grouped together
int 2147483647 [ [ -∞ ∞ ] ]
If non-zero, partitions VCF output into shards, each containing up to the given number of records.
int 0 [ [ 0 ∞ ] ]
Minimum genotype QUAL score for each trio member required to accept a site as a violation. Default is 50.
double 50.0 [ [ -∞ ∞ ] ]
If provided, all -eval tracks will be merged into a single eval track
If true, VariantEval will treat -eval 1 -eval 2 as separate tracks from the same underlying
variant set, and evaluate the union of the results. Useful when you want to do -eval chr1.vcf -eval chr2.vcf etc.
boolean false
Minimum phasing quality
double 10.0 [ [ -∞ ∞ ] ]
File to which variants should be written
R File null
Pedigree file for determining the population "founders"
GATKPath null
The strictness for validating the pedigree. Can be either STRICT or SILENT. Default is STRICT
The --pedigreeValidationType argument is an enumerated type (PedigreeValidationType), which can have one of the following values:
PedigreeValidationType STRICT
Whether to suppress job-summary info on System.err.
Boolean false
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
Number of bases on either side to expand spanning reference window
int 1 [ [ -∞ ∞ ] ]
Reference sequence file
R GATKPath null
If provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping
boolean false
Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context
Set[String] []
Per-sample ploidy (number of chromosomes per sample)
int 2 [ [ -∞ ∞ ] ]
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
One or more stratifications to use when evaluating the data
ArrayList[String] []
Names to use for the list of stratifications (must be a 1-to-1 mapping)
ArrayList[String] []
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
File containing tribble-readable features for the IntervalStratificiation
File containing tribble-readable features for the IntervalStratificiation
FeatureInput[Feature] null
One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified)
List[String] []
Temp directory to use.
GATKPath null
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
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
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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.