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.gatkreport: ##: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 -Xmx2g -jar GenomeAnalysisTK.jar \ -R ref.fasta \ -T VariantEval \ -o output.eval.gatkreport \ --eval:set1 set1.vcf \ --eval:set2 set2.vcf \ [--comp comp.vcf]
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.
The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
| Name | Type | Default value | Summary |
|---|---|---|---|
| Required | |||
| --eval | List[RodBinding[VariantContext]] | NA | Input evaluation file(s) |
| Optional | |||
| --ancestralAlignments | File | NA | Fasta file with ancestral alleles |
| --comp | List[RodBinding[VariantContext]] | [] | Input comparison file(s) |
| --dbsnp | RodBinding[VariantContext] | none | dbSNP file |
| --doNotUseAllStandardModules | Boolean | false | Do not use the standard modules by default (instead, only those that are specified with the -EV option) |
| --evalModule | String[] | [] | One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noEV is specified) |
| --goldStandard | RodBinding[VariantContext] | none | Evaluations that count calls at sites of true variation (e.g., indel calls) will use this argument as their gold standard for comparison |
| --keepAC0 | boolean | false | If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes |
| --known_names | HashSet[String] | [] | Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets |
| --knownCNVs | IntervalBinding[Feature] | NA | File containing tribble-readable features describing a known list of copy number variants |
| --list | Boolean | false | List the available eval modules and exit |
| --mergeEvals | boolean | false | If provided, all -eval tracks will be merged into a single eval track |
| --minPhaseQuality | double | 10.0 | Minimum phasing quality |
| -mvq | double | 50.0 | Minimum genotype QUAL score for each trio member required to accept a site as a violation. Default is 50. |
| -noST | Boolean | false | Do not use the standard stratification modules by default (instead, only those that are specified with the -S option) |
| --out | PrintStream | stdout | An output file created by the walker. Will overwrite contents if file exists |
| --requireStrictAlleleMatch | boolean | false | If provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping |
| --sample | Set[String] | NA | Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context |
| --samplePloidy | int | 2 | Per-sample ploidy (number of chromosomes per sample) |
| --select_exps | ArrayList[String] | [] | One or more stratifications to use when evaluating the data |
| --select_names | ArrayList[String] | [] | Names to use for the list of stratifications (must be a 1-to-1 mapping) |
| --stratificationModule | String[] | [] | One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified) |
| --stratIntervals | IntervalBinding[Feature] | NA | File containing tribble-readable features for the IntervalStratificiation |
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.
Input comparison file(s). The variant file(s) to compare against. --comp binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3
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. --dbsnp binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3
Do not use the standard modules by default (instead, only those that are specified with the -EV option).
Input evaluation file(s). The variant file(s) to evaluate. --eval binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3
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.
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 --goldStandard binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3
If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes.
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.
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.
List the available eval modules and exit. Note that the --list argument requires a fully resolved and correct command-line to work.
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.
Minimum phasing quality.
Minimum genotype QUAL score for each trio member required to accept a site as a violation. Default is 50..
Do not use the standard stratification modules by default (instead, only those that are specified with the -S option).
An output file created by the walker. Will overwrite contents if file exists.
If provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping.
Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context.
Per-sample ploidy (number of chromosomes per sample).
One or more stratifications to use when evaluating the data.
Names to use for the list of stratifications (must be a 1-to-1 mapping).
One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified).
File containing tribble-readable features for the IntervalStratificiation. File containing tribble-readable features for the IntervalStratificiation
See also Guide Index | Technical Documentation Index | Support Forum
GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.
