Call germline SNPs and indels via local re-assembly of haplotypes
java -jar GenomeAnalysisTK.jar -R reference.fasta -T HaplotypeCaller -I sample1.bam --emitRefConfidence GVCF [--dbsnp dbSNP.vcf] [-L targets.interval_list] -o output.raw.snps.indels.g.vcf
Argument name(s) | Default value | Summary | |
---|---|---|---|
Optional Inputs | |||
--alleles | none | Set of alleles to use in genotyping | |
--dbsnp  -D | none | dbSNP file | |
Optional Outputs | |||
--activeRegionOut  -ARO | NA | Output the active region to this IGV formatted file | |
--activityProfileOut  -APO | NA | Output the raw activity profile results in IGV format | |
--graphOutput  -graph | NA | Write debug assembly graph information to this file | |
--out  -o | stdout | File to which variants should be written | |
Optional Parameters | |||
--contamination_fraction_to_filter  -contamination | 0.0 | Fraction of contamination to aggressively remove | |
--genotyping_mode  -gt_mode | DISCOVERY | Specifies how to determine the alternate alleles to use for genotyping | |
--group  -G | [StandardAnnotation, StandardHCAnnotation] | 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 | |
--maxReadsInRegionPerSample | 10000 | Maximum reads in an active region | |
--min_base_quality_score  -mbq | 10 | Minimum base quality required to consider a base for calling | |
--minReadsPerAlignmentStart  -minReadsPerAlignStart | 10 | Minimum number of reads sharing the same alignment start for each genomic location in an active region | |
--sample_name  -sn | NA | Name of single sample to use from a multi-sample bam | |
--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 | |
--useNewAFCalculator  -newQual | false | Use new AF model instead of the so-called exact model | |
Advanced Inputs | |||
--activeRegionIn  -AR | NA | Use this interval list file as the active regions to process | |
--comp | [] | Comparison VCF file | |
Advanced Outputs | |||
--bamOutput  -bamout | NA | File to which assembled haplotypes should be written | |
Advanced Parameters | |||
--activeProbabilityThreshold  -ActProbThresh | 0.002 | Threshold for the probability of a profile state being active. | |
--activeRegionExtension | NA | The active region extension; if not provided defaults to Walker annotated default | |
--activeRegionMaxSize | NA | The active region maximum size; if not provided defaults to Walker annotated default | |
--annotation  -A | [] | One or more specific annotations to apply to variant calls | |
--bamWriterType | CALLED_HAPLOTYPES | Which haplotypes should be written to the BAM | |
--bandPassSigma | NA | The sigma of the band pass filter Gaussian kernel; if not provided defaults to Walker annotated default | |
--contamination_fraction_per_sample_file  -contaminationFile | NA | Contamination per sample | |
--emitRefConfidence  -ERC | false | Mode for emitting reference confidence scores | |
--excludeAnnotation  -XA | [] | One or more specific annotations to exclude | |
--gcpHMM | 10 | Flat gap continuation penalty for use in the Pair HMM | |
--GVCFGQBands  -GQB | [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] | Exclusive upper bounds for reference confidence GQ bands (must be in [1, 100] and specified in increasing order) | |
--indelSizeToEliminateInRefModel  -ERCIS | 10 | The size of an indel to check for in the reference model | |
--input_prior  -inputPrior | [] | Input prior for calls | |
--kmerSize | [10, 25] | Kmer size to use in the read threading assembler | |
--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 | |
--maxNumHaplotypesInPopulation | 128 | Maximum number of haplotypes to consider for your population | |
--maxReadsInMemoryPerSample | 30000 | Maximum reads per sample given to traversal map() function | |
--maxTotalReadsInMemory | 10000000 | Maximum total reads given to traversal map() function | |
--minDanglingBranchLength | 4 | Minimum length of a dangling branch to attempt recovery | |
--minPruning | 2 | Minimum support to not prune paths in the graph | |
--numPruningSamples | 1 | Number of samples that must pass the minPruning threshold | |
--output_mode  -out_mode | EMIT_VARIANTS_ONLY | Which type of calls we should output | |
--pcr_indel_model  -pcrModel | CONSERVATIVE | The PCR indel model to use | |
--phredScaledGlobalReadMismappingRate  -globalMAPQ | 45 | The global assumed mismapping rate for reads | |
Advanced Flags | |||
--allowNonUniqueKmersInRef | false | Allow graphs that have non-unique kmers in the reference | |
--allSitePLs | false | Annotate all sites with PLs | |
--consensus | false | 1000G consensus mode | |
--debug | false | Print out very verbose debug information about each triggering active region | |
--disableOptimizations | false | Don't skip calculations in ActiveRegions with no variants | |
--doNotRunPhysicalPhasing | false | Disable physical phasing | |
--dontIncreaseKmerSizesForCycles | false | Disable iterating over kmer sizes when graph cycles are detected | |
--dontTrimActiveRegions | false | If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping | |
--dontUseSoftClippedBases | false | Do not analyze soft clipped bases in the reads | |
--emitDroppedReads  -edr | false | Emit reads that are dropped for filtering, trimming, realignment failure | |
--forceActive | false | If provided, all bases will be tagged as active | |
--useAllelesTrigger  -allelesTrigger | false | Use additional trigger on variants found in an external alleles file | |
--useFilteredReadsForAnnotations | false | Use the contamination-filtered read maps for the purposes of annotating variants |