java -jar GenomeAnalysisTK.jar

Category

Genome Variant Analysis

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Usage

java -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R reference.fasta --variant sample1.g.vcf --variant sample2.g.vcf -o output.vcf

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Manual

Argument name(s)	Default value	Summary
Required Inputs
--variant  -V	NA	One or more input gVCF files
Optional Inputs
--dbsnp  -D	none	dbSNP file
Optional Outputs
--out  -o	stdout	File to which variants should be written
Optional Parameters
--group  -G	[StandardAnnotation]	One or more classes/groups of annotations to apply to variant calls
--heterozygosity  -hets	0.001	Heterozygosity value used to compute prior likelihoods for any locus
--heterozygosity_stdev  -heterozygosityStandardDeviation	0.01	Standard deviation of eterozygosity for SNP and indel calling.
--indel_heterozygosity  -indelHeterozygosity	1.25E-4	Heterozygosity for indel calling
--sample_ploidy  -ploidy	2	Ploidy per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).
--standard_min_confidence_threshold_for_calling  -stand_call_conf	10.0	The minimum phred-scaled confidence threshold at which variants should be called
Optional Flags
--annotateNDA  -nda	false	Annotate number of alleles observed
--includeNonVariantSites  -allSites	false	Include loci found to be non-variant after genotyping
--useNewAFCalculator  -newQual	false	Use new AF model instead of the so-called exact model
Advanced Parameters
--annotation  -A	[]	One or more specific annotations to recompute. The single value 'none' removes the default annotations
--input_prior  -inputPrior	[]	Input prior for calls
--max_alternate_alleles  -maxAltAlleles	6	Maximum number of alternate alleles to genotype
--max_genotype_count  -maxGT	1024	Maximum number of genotypes to consider at any site
--max_num_PL_values  -maxNumPLValues	100	Maximum number of PL values to output

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