java -jar GenomeAnalysisTK.jar -T IndelRealigner -R reference.fasta -I input.bam -known indels.vcf -targetIntervals intervalListFromRTC.intervals -o realignedBam.bam
Argument name(s) | Default value | Summary | |
---|---|---|---|
Required Inputs | |||
--targetIntervals | NA | Intervals file output from RealignerTargetCreator | |
Optional Inputs | |||
--knownAlleles  -known | [] | Input VCF file(s) with known indels | |
Optional Outputs | |||
--out  -o | NA | Output bam | |
Optional Parameters | |||
--consensusDeterminationModel  -model | USE_READS | Determines how to compute the possible alternate consenses | |
--LODThresholdForCleaning  -LOD | 5.0 | LOD threshold above which the cleaner will clean | |
--nWayOut | NA | Generate one output file for each input (-I) bam file (not compatible with -output) | |
Advanced Parameters | |||
--entropyThreshold  -entropy | 0.15 | Percentage of mismatches at a locus to be considered having high entropy (0.0 | |
--maxConsensuses | 30 | Max alternate consensuses to try (necessary to improve performance in deep coverage) | |
--maxIsizeForMovement  -maxIsize | 3000 | maximum insert size of read pairs that we attempt to realign | |
--maxPositionalMoveAllowed  -maxPosMove | 200 | Maximum positional move in basepairs that a read can be adjusted during realignment | |
--maxReadsForConsensuses  -greedy | 120 | Max reads used for finding the alternate consensuses (necessary to improve performance in deep coverage) | |
--maxReadsForRealignment  -maxReads | 20000 | Max reads allowed at an interval for realignment | |
--maxReadsInMemory  -maxInMemory | 150000 | max reads allowed to be kept in memory at a time by the SAMFileWriter | |
Advanced Flags | |||
--noOriginalAlignmentTags  -noTags | false | Don't output the original cigar or alignment start tags for each realigned read in the output bam |