Category

Genome Variant Analysis


Usage

java -jar GenomeAnalysisTK.jar -T ValidationSiteSelectorWalker -R reference.fasta -V:foo input1.vcf -V:bar input2.vcf --numValidationSites 200 -sf samples.txt -o output.vcf -sampleMode POLY_BASED_ON_GT -freqMode UNIFORM -selectType INDEL


Manual

Argument name(s)Default valueSummary
Required Inputs
--variant
 -V
NAInput VCF file, can be specified multiple times
Required Parameters
--numValidationSites
 -numSites
0Number of output validation sites
Optional Inputs
--sample_file
 -sf
NAFile containing a list of samples (one per line) to include. Can be specified multiple times
Optional Outputs
--out
 -o
stdoutFile to which variants should be written
Optional Parameters
--frequencySelectionMode
 -freqMode
KEEP_AF_SPECTRUMAllele Frequency selection mode
--sample_expressions
 -se
NARegular expression to select many samples from the ROD tracks provided. Can be specified multiple times
--sample_name
 -sn
[]Include genotypes from this sample. Can be specified multiple times
--sampleMode
NONESample selection mode
--samplePNonref
0.99GL-based selection mode only: the probability that a site is non-reference in the samples for which to include the site
--selectTypeToInclude
 -selectType
[]Select only a certain type of variants from the input file. Valid types are INDEL, SNP, MIXED, MNP, SYMBOLIC, NO_VARIATION. Can be specified multiple times
Optional Flags
--ignoreGenotypes
falseIf true, will ignore genotypes in VCF, will take AC,AF from annotations and will make no sample selection
--ignorePolymorphicStatus
falseIf true, will ignore polymorphic status in VCF, and will take VCF record directly without pre-selection
--includeFilteredSites
 -ifs
falseIf true, will include filtered sites in set to choose variants from


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