Call somatic SNPs and indels via local re-assembly of haplotypes
java -jar GenomeAnalysisTK.jar -T MuTect2 -R reference.fasta -I:tumor tumor.bam -I:normal normal.bam [--dbsnp dbSNP.vcf] [--cosmic COSMIC.vcf] [-L targets.interval_list] -o output.vcf
Argument name(s) | Default value | Summary | |
---|---|---|---|
Optional Inputs | |||
--alleles | none | Set of alleles to use in genotyping | |
--cosmic | [] | VCF file of COSMIC sites | |
--dbsnp  -D | none | dbSNP file | |
--normal_panel  -PON | [] | VCF file of sites observed in normal | |
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 | |
--dbsnp_normal_lod | 5.5 | LOD threshold for calling normal non-variant at dbsnp sites | |
--debug_read_name | NA | trace this read name through the calling process | |
--genotyping_mode  -gt_mode | DISCOVERY | Specifies how to determine the alternate alleles to use for genotyping | |
--group  -G | [] | 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 | |
--initial_normal_lod | 0.5 | Initial LOD threshold for calling normal variant | |
--initial_tumor_lod | 4.0 | Initial LOD threshold for calling tumor variant | |
--max_alt_allele_in_normal_fraction | 0.03 | Threshold for maximum alternate allele fraction in normal | |
--max_alt_alleles_in_normal_count | 1 | Threshold for maximum alternate allele counts in normal | |
--max_alt_alleles_in_normal_qscore_sum | 20 | Threshold for maximum alternate allele quality score sum in normal | |
--maxReadsInRegionPerSample | 1000 | Maximum reads in an active region | |
--min_base_quality_score  -mbq | 10 | Minimum base quality required to consider a base for calling | |
--minReadsPerAlignmentStart  -minReadsPerAlignStart | 5 | Minimum number of reads sharing the same alignment start for each genomic location in an active region | |
--normal_lod | 2.2 | LOD threshold for calling normal non-germline | |
--pir_mad_threshold | 3.0 | threshold for clustered read position artifact MAD | |
--pir_median_threshold | 10.0 | threshold for clustered read position artifact median | |
--power_constant_qscore | 30 | Phred scale quality score constant to use in power calculations | |
--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 | |
--tumor_lod | 6.3 | LOD threshold for calling tumor variant | |
Optional Flags | |||
--annotateNDA Â -nda | false | Annotate number of alleles observed | |
--enable_clustered_read_position_filter | false | turn on clustered read position filter | |
--enable_strand_artifact_filter | false | turn on strand artifact filter | |
--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 | [DepthPerAlleleBySample, BaseQualitySumPerAlleleBySample, TandemRepeatAnnotator, OxoGReadCounts] | 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 | NONE | Mode for emitting reference confidence scores | |
--excludeAnnotation  -XA | [SpanningDeletions] | One or more specific annotations to exclude | |
--gcpHMM | 10 | Flat gap continuation penalty for use in the Pair HMM | |
--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 | |
--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 | |
--artifact_detection_mode | false | Enable artifact detection for creating panels of normals | |
--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 | If specified, we will 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 | |
--m2debug | false | Print out very verbose M2 debug information | |
--useFilteredReadsForAnnotations | false | Use the contamination-filtered read maps for the purposes of annotating variants |