java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V input.vcf -o output.vcf -sn SAMPLE_A_PARC -sn SAMPLE_B_ACTG
Argument name(s) | Default value | Summary | |
---|---|---|---|
Required Inputs | |||
--variant  -V | NA | Input VCF file | |
Optional Inputs | |||
--concordance  -conc | none | Output variants also called in this comparison track | |
--discordance  -disc | none | Output 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 | NA | File containing a list of samples to include | |
Optional Outputs | |||
--out  -o | stdout | File to which variants should be written | |
Optional Parameters | |||
--exclude_sample_name  -xl_sn | [] | Exclude genotypes from this sample | |
--excludeIDs  -xlIDs | NA | List of variant IDs to select | |
--keepIDs  -IDs | NA | List of variant IDs to select | |
--maxFilteredGenotypes | 2147483647 | Maximum number of samples filtered at the genotype level | |
--maxFractionFilteredGenotypes | 1.0 | Maximum fraction of samples filtered at the genotype level | |
--maxIndelSize | 2147483647 | Maximum size of indels to include | |
--maxNOCALLfraction | 1.0 | Maximum fraction of samples with no-call genotypes | |
--maxNOCALLnumber | 2147483647 | Maximum number of samples with no-call genotypes | |
--mendelianViolationQualThreshold  -mvq | 0.0 | Minimum GQ score for each trio member to accept a site as a violation | |
--minFilteredGenotypes | 0 | Minimum number of samples filtered at the genotype level | |
--minFractionFilteredGenotypes | 0.0 | Maximum fraction of samples filtered at the genotype level | |
--minIndelSize | 0 | Minimum size of indels to include | |
--remove_fraction_genotypes  -fractionGenotypes | 0.0 | Select a fraction of genotypes at random from the input and sets them to no-call | |
--restrictAllelesTo | ALL | Select only variants of a particular allelicity | |
--sample_expressions  -se | NA | Regular expression to select multiple samples | |
--sample_name  -sn | [] | Include genotypes from this sample | |
--select_random_fraction  -fraction | 0.0 | Select 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 | false | Don't include filtered sites | |
--excludeNonVariants  -env | false | Don't include non-variant sites | |
--forceValidOutput | false | Forces output VCF to be compliant to up-to-date version | |
--invertMendelianViolation  -invMv | false | Output non-mendelian violation sites only | |
--invertselect  -invertSelect | false | Invert the selection criteria for -select | |
--keepOriginalAC | false | Store the original AC, AF, and AN values after subsetting | |
--keepOriginalDP | false | Store the original DP value after subsetting | |
--mendelianViolation  -mv | false | Output mendelian violation sites only | |
--preserveAlleles  -noTrim | false | Preserve original alleles, do not trim | |
--removeUnusedAlternates  -trimAlternates | false | Remove alternate alleles not present in any genotypes | |
--setFilteredGtToNocall | false | Set filtered genotypes to no-call |