Category

Genome Variant Analysis


Usage

java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V myCalls.vcf --concordance theirCalls.vcf -o output.vcf -sn mySample


Manual

Argument name(s)Default valueSummary
Required Inputs
--variant
 -V
NAInput VCF file
Optional Inputs
--concordance
 -conc
noneOutput variants also called in this comparison track
--discordance
 -disc
noneOutput variants not called in this comparison track
--exclude_sample_expressions
 -xl_se
[]List of sample expressions to exclude
--exclude_sample_file
 -xl_sf
[]List of samples to exclude
--sample_file
 -sf
NAFile containing a list of samples to include
Optional Outputs
--out
 -o
stdoutFile to which variants should be written
Optional Parameters
--exclude_sample_name
 -xl_sn
[]Exclude genotypes from this sample
--excludeIDs
 -xlIDs
NAList of variant IDs to select
--keepIDs
 -IDs
NAList of variant IDs to select
--maxFilteredGenotypes
2147483647Maximum number of samples filtered at the genotype level
--maxFractionFilteredGenotypes
1.0Maximum fraction of samples filtered at the genotype level
--maxIndelSize
2147483647Maximum size of indels to include
--maxNOCALLfraction
1.0Maximum fraction of samples with no-call genotypes
--maxNOCALLnumber
2147483647Maximum number of samples with no-call genotypes
--mendelianViolationQualThreshold
 -mvq
0.0Minimum GQ score for each trio member to accept a site as a violation
--minFilteredGenotypes
0Minimum number of samples filtered at the genotype level
--minFractionFilteredGenotypes
0.0Maximum fraction of samples filtered at the genotype level
--minIndelSize
0Minimum size of indels to include
--remove_fraction_genotypes
 -fractionGenotypes
0.0Select a fraction of genotypes at random from the input and sets them to no-call
--restrictAllelesTo
ALLSelect only variants of a particular allelicity
--sample_expressions
 -se
NARegular expression to select multiple samples
--sample_name
 -sn
[]Include genotypes from this sample
--select_random_fraction
 -fraction
0.0Select a fraction of variants at random from the input
--selectexpressions
 -select
[]One or more criteria to use when selecting the data
--selectTypeToExclude
 -xlSelectType
[]Do not select certain type of variants from the input file
--selectTypeToInclude
 -selectType
[]Select only a certain type of variants from the input file
Optional Flags
--excludeFiltered
 -ef
falseDon't include filtered sites
--excludeNonVariants
 -env
falseDon't include non-variant sites
--forceValidOutput
falseForces output VCF to be compliant to up-to-date version
--invertMendelianViolation
 -invMv
falseOutput non-mendelian violation sites only
--invertselect
 -invertSelect
falseInvert the selection criteria for -select
--keepOriginalAC
falseStore the original AC, AF, and AN values after subsetting
--keepOriginalDP
falseStore the original DP value after subsetting
--mendelianViolation
 -mv
falseOutput mendelian violation sites only
--preserveAlleles
 -noTrim
falsePreserve original alleles, do not trim
--removeUnusedAlternates
 -trimAlternates
falseRemove alternate alleles not present in any genotypes
--setFilteredGtToNocall
falseSet filtered genotypes to no-call


Share your experience or ask a question