General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)
java -jar GenomeAnalysisTK.jar -T VariantEval -R reference.fasta -o output.eval.grp --eval:set1 set1.vcf --eval:set2 set2.vcf [--comp comp.vcf]
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 |