General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)
Category Variant Evaluation and Refinement
Overview
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.
Input
One or more variant sets to evaluate plus any number of comparison sets.
Output
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 ... ...
Usage examples
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
Caveat
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.
VariantEval 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 | |||
| --eval |
[] | Input evaluation file(s) | |
| --output -O |
null | File to which variants should be written | |
| Optional Tool Arguments | |||
| --ancestral-alignments -aa |
null | 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). | |
| --comp |
[] | Input comparison file(s) | |
| --dbsnp -D |
null | 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 -noEV 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. | |
| --gold-standard -gold |
null | 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 |
null | File containing tribble-readable features describing a known list of copy number variants | |
| --KNOWN_NAMES -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 |
null | Pedigree file for determining the population "founders" | |
| --reference -R |
null | Reference sequence | |
| --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) | |
| --SELECT_EXPS -select |
[] | One or more stratifications to use when evaluating the data | |
| --SELECT_NAMES -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 |
null | 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 |
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-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 | |
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
--ancestral-alignments / -aa
Fasta file with ancestral alleles
File null
--arguments_file / NA
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 [ [ -∞ ∞ ] ]
--comp / -comp
Input comparison file(s)
The variant file(s) to compare against.
List[FeatureInput[VariantContext]] []
--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-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
--do-not-use-all-standard-modules / -no-ev
Do not use the standard modules by default (instead, only those that are specified with the -EV option)
Boolean false
--do-not-use-all-standard-stratifications / -no-st
Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)
Boolean false
--eval / -eval
Input evaluation file(s)
The variant file(s) to evaluate.
R List[FeatureInput[VariantContext]] []
--eval-module / -EV
One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noEV is specified)
See the -list argument to view available modules.
List[String] []
--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] []
--gatk-config-file / NA
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 / NA
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.
String ""
--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
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
--help / -h
display the help message
boolean false
--input / -I
BAM/SAM/CRAM file containing reads
List[String] []
--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] []
--keep-ac0 / -keep-ac0
If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes
boolean false
--known-cnvs / -known-cnvs
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
--KNOWN_NAMES / -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 of feature tracks to be used for specifying "known" variants other than dbSNP.
HashSet[String] []
--lenient / -LE
Lenient processing of VCF files
boolean false
--list / -ls
List the available eval modules and exit
Note that the --list argument requires a fully resolved and correct command-line to work.
Boolean false
--mendelian-violation-qual-threshold / -mvq
Minimum genotype QUAL score for each trio member required to accept a site as a violation. Default is 50.
double 50.0 [ [ -∞ ∞ ] ]
--merge-evals / -merge-evals
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
--min-phase-quality / -mpq
Minimum phasing quality
double 10.0 [ [ -∞ ∞ ] ]
--output / -O
File to which variants should be written
R File null
--pedigree / -ped
Pedigree file for determining the population "founders"
File null
--QUIET / NA
Whether to suppress job-summary info on System.err.
Boolean false
--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[String] []
--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
String null
--require-strict-allele-match / -strict
If provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping
boolean false
--sample / -sn
Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context
Set[String] []
--sample-ploidy / -ploidy
Per-sample ploidy (number of chromosomes per sample)
int 2 [ [ -∞ ∞ ] ]
--seconds-between-progress-updates / -seconds-between-progress-updates
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
--SELECT_EXPS / -select
One or more stratifications to use when evaluating the data
ArrayList[String] []
--SELECT_NAMES / -select-name
Names to use for the list of stratifications (must be a 1-to-1 mapping)
ArrayList[String] []
--sequence-dictionary / -sequence-dictionary
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
String null
--showHidden / -showHidden
display hidden arguments
boolean false
--sites-only-vcf-output / NA
If true, don't emit genotype fields when writing vcf file output.
boolean false
--strat-intervals / -strat-intervals
File containing tribble-readable features for the IntervalStratificiation
File containing tribble-readable features for the IntervalStratificiation
FeatureInput[Feature] null
--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)
List[String] []
--tmp-dir / NA
Temp directory to use.
String 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
--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
--version / NA
display the version number for this tool
boolean false
GATK version 4.1.1.0 built at Sat, 23 Nov 2019 17:58:14 -0500.
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