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 singletons 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 CompRod CpG EvalRod 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 ... ...
java -jar GenomeAnalysisTK.jar \ -T 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)
Java -jar GenomeAnalysisTK.jar \ -T VariantEval \ -R reference.fasta \ -o output.MVs.byFamily.table \ --eval multiFamilyCallset.vcf \ -noEV -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.
These Read Filters are automatically applied to the data by the Engine before processing by VariantEval.
This tool can be run in multi-threaded mode using this option.
This tool uses a sliding window on the reference.
All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.
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 Inputs | |||
| --eval |
NA | Input evaluation file(s) | |
| Optional Inputs | |||
| --comp |
[] | Input comparison file(s) | |
| --dbsnp -D |
none | dbSNP file | |
| --goldStandard -gold |
none | Evaluations that count calls at sites of true variation (e.g., indel calls) will use this argument as their gold standard for comparison | |
| --knownCNVs |
NA | File containing tribble-readable features describing a known list of copy number variants | |
| --stratIntervals |
NA | File containing tribble-readable features for the IntervalStratificiation | |
| Optional Outputs | |||
| --out -o |
stdout | An output file created by the walker. Will overwrite contents if file exists | |
| Optional Parameters | |||
| --ancestralAlignments -aa |
NA | Fasta file with ancestral alleles | |
| --evalModule -EV |
[] | One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noEV is specified) | |
| --known_names -knownName |
[] | Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets | |
| --mendelianViolationQualThreshold -mvq |
50.0 | Minimum genotype QUAL score for each trio member required to accept a site as a violation. Default is 50. | |
| --minPhaseQuality -mpq |
10.0 | Minimum phasing quality | |
| --sample -sn |
NA | Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context | |
| --samplePloidy -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 -selectName |
[] | Names to use for the list of stratifications (must be a 1-to-1 mapping) | |
| --stratificationModule -ST |
[] | One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified) | |
| Optional Flags | |||
| --doNotUseAllStandardModules -noEV |
false | Do not use the standard modules by default (instead, only those that are specified with the -EV option) | |
| --doNotUseAllStandardStratifications -noST |
false | Do not use the standard stratification modules by default (instead, only those that are specified with the -S option) | |
| --keepAC0 |
false | If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes | |
| --list -ls |
false | List the available eval modules and exit | |
| --mergeEvals |
false | If provided, all -eval tracks will be merged into a single eval track | |
| --requireStrictAlleleMatch -strict |
false | If provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping | |
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.
Fasta file with ancestral alleles
File NA
Input comparison file(s)
The variant file(s) to compare against.
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
List[RodBinding[VariantContext]] []
dbSNP file
dbSNP comparison VCF. By default, the dbSNP file is used to specify the set of "known" variants.
Other sets can be specified with the -knownName (--known_names) argument.
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
RodBinding[VariantContext] none
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.
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
R List[RodBinding[VariantContext]] NA
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.
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
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
RodBinding[VariantContext] none
If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes
boolean false
Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets
List of rod tracks to be used for specifying "known" variants other than dbSNP.
HashSet[String] []
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.
IntervalBinding[Feature] NA
List the available eval modules and exit
Note that the --list argument requires a fully resolved and correct command-line to work.
Boolean false
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 [ [ -∞ ∞ ] ]
An output file created by the walker. Will overwrite contents if file exists
PrintStream stdout
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] NA
Per-sample ploidy (number of chromosomes per sample)
int 2 [ [ -∞ ∞ ] ]
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] []
One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified)
String[] []
File containing tribble-readable features for the IntervalStratificiation
File containing tribble-readable features for the IntervalStratificiation
IntervalBinding[Feature] NA