What it does

A variant caller which unifies the approaches of several disparate callers. Works for single-sample and multi-sample data. The user can choose from several different incorporated calculation models.

For more information on the GATK Unified Genotyper, see this tool specific page.

To learn about best practices for variant detection using GATK, see this overview.

If you encounter errors, please view the GATK FAQ.

Inputs

GenomeAnalysisTK: UnifiedGenotyper accepts an aligned BAM input file.

Outputs

The output is in VCF format.

Go here for details on GATK file formats.

Settings:

genotype_likelihoods_model                        Genotype likelihoods calculation model to employ -- BOTH is the default option, while INDEL is also available for calling indels and SNP is available for calling SNPs only (SNP|INDEL|BOTH)
p_nonref_model                                    Non-reference probability calculation model to employ -- EXACT is the default option, while GRID_SEARCH is also available. (EXACT|GRID_SEARCH)
heterozygosity                                    Heterozygosity value used to compute prior likelihoods for any locus
pcr_error_rate                                    The PCR error rate to be used for computing fragment-based likelihoods
genotyping_mode                                   Should we output confident genotypes (i.e. including ref calls) or just the variants? (DISCOVERY|GENOTYPE_GIVEN_ALLELES)
output_mode                                       Should we output confident genotypes (i.e. including ref calls) or just the variants? (EMIT_VARIANTS_ONLY|EMIT_ALL_CONFIDENT_SITES|EMIT_ALL_SITES)
standard_min_confidence_threshold_for_calling     The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called
standard_min_confidence_threshold_for_emitting    The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)
noSLOD                                            If provided, we will not calculate the SLOD
min_base_quality_score                            Minimum base quality required to consider a base for calling
max_deletion_fraction                             Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05]
min_indel_count_for_genotyping                    Minimum number of consensus indels required to trigger genotyping run
indel_heterozygosity                              Heterozygosity for indel calling
indelGapContinuationPenalty                       Indel gap continuation penalty
indelGapOpenPenalty                               Indel gap open penalty
indelHaplotypeSize                                Indel haplotype size
doContextDependentGapPenalties                    Vary gap penalties by context
indel_recal_file                                  Filename for the input covariates table recalibration .csv file - EXPERIMENTAL, DO NO USE
indelDebug                                        Output indel debug info
out                                               File to which variants should be written
annotation                                        One or more specific annotations to apply to variant calls
group                                             One or more classes/groups of annotations to apply to variant calls

Citation

For the underlying tool, please cite DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8.

If you use this tool in Galaxy, please cite Blankenberg D, et al. In preparation.