java -jar GenomeAnalysisTK.jar

Category

Genome Variant Analysis

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Usage

java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R reference.fasta -I input.bam -o raw_variants.vcf --output_mode EMIT_ALL_SITES

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Manual

Argument name(s)	Default value	Summary
Optional Inputs
--alleles	none	Set of alleles to use in genotyping
--comp	[]	Comparison VCF file
--dbsnp  -D	none	dbSNP file
Optional Outputs
--out  -o	stdout	File to which variants should be written
Optional Parameters
--annotation  -A	[]	One or more specific annotations to apply to variant calls
--contamination_fraction_to_filter  -contamination	0.0	Fraction of contamination to aggressively remove
--excludeAnnotation  -XA	[]	One or more specific annotations to exclude
--genotype_likelihoods_model  -glm	SNP	Genotype likelihoods calculation model to employ -- SNP is the default option, while INDEL is also available for calling indels and BOTH is available for calling both together
--genotyping_mode  -gt_mode	DISCOVERY	Specifies how to determine the alternate alleles to use for genotyping
--group  -G	[Standard, StandardUG]	One or more classes/groups of annotations to apply to variant calls. The single value 'none' removes the default group
--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
--max_deletion_fraction  -deletions	0.05	Maximum fraction of reads with deletions spanning this locus for it to be callable
--min_base_quality_score  -mbq	17	Minimum base quality required to consider a base for calling
--min_indel_count_for_genotyping  -minIndelCnt	5	Minimum number of consensus indels required to trigger genotyping run
--min_indel_fraction_per_sample  -minIndelFrac	0.25	Minimum fraction of all reads at a locus that must contain an indel (of any allele) for that sample to contribute to the indel count for alleles
--pair_hmm_implementation  -pairHMM	LOGLESS_CACHING	The PairHMM implementation to use for -glm INDEL genotype likelihood calculations
--pcr_error_rate  -pcr_error	1.0E-4	The PCR error rate to be used for computing fragment-based likelihoods
--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
--computeSLOD  -slod	false	If provided, we will calculate the SLOD (SB annotation)
--useNewAFCalculator  -newQual	false	Use new AF model instead of the so-called exact model
Advanced Parameters
--contamination_fraction_per_sample_file  -contaminationFile	NA	Contamination per sample
--indelGapContinuationPenalty  -indelGCP	10	Indel gap continuation penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10
--indelGapOpenPenalty  -indelGOP	45	Indel gap open penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10
--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
--onlyEmitSamples	[]	If provided, only these samples will be emitted into the VCF, regardless of which samples are present in the BAM file
--output_mode  -out_mode	EMIT_VARIANTS_ONLY	Which type of calls we should output
Advanced Flags
--allSitePLs	false	Annotate all sites with PLs

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