Category

Genome Variant Analysis


Usage

Java -jar GenomeAnalysisTK.jar -T VariantEval -R reference.fasta -o output.MVs.byFamily.table --eval multiFamilyCallset.vcf -noEV -noST -ST Family -EV MendelianViolationEvaluator


Manual

Argument name(s)Default valueSummary
Required Inputs
--eval
NAInput evaluation file(s)
Optional Inputs
--comp
[]Input comparison file(s)
--dbsnp
 -D
nonedbSNP file
--goldStandard
 -gold
noneEvaluations that count calls at sites of true variation (e.g., indel calls) will use this argument as their gold standard for comparison
--knownCNVs
NAFile containing tribble-readable features describing a known list of copy number variants
--stratIntervals
NAFile containing tribble-readable features for the IntervalStratificiation
Optional Outputs
--out
 -o
stdoutAn output file created by the walker. Will overwrite contents if file exists
Optional Parameters
--ancestralAlignments
 -aa
NAFasta 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
50.0Minimum genotype QUAL score for each trio member required to accept a site as a violation. Default is 50.
--minPhaseQuality
 -mpq
10.0Minimum phasing quality
--sample
 -sn
NADerive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context
--samplePloidy
 -ploidy
2Per-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
falseDo not use the standard modules by default (instead, only those that are specified with the -EV option)
--doNotUseAllStandardStratifications
 -noST
falseDo not use the standard stratification modules by default (instead, only those that are specified with the -S option)
--keepAC0
falseIf provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes
--list
 -ls
falseList the available eval modules and exit
--mergeEvals
falseIf provided, all -eval tracks will be merged into a single eval track
--requireStrictAlleleMatch
 -strict
falseIf provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping


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