java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R reference.fasta -I sample1.bam [-I sample2.bam ...] --dbsnp dbSNP.vcf -o snps.raw.vcf -stand_call_conf [50.0] [-L targets.interval_list]
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 Â -nda | false | Annotate number of alleles observed | |
--computeSLOD Â -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 |