Category

Genome Variant Analysis


Usage

java -jar GenomeAnalysisTK.jar -T IndelRealigner -R reference.fasta -I input.bam -known indels.vcf -targetIntervals intervalListFromRTC.intervals -o realignedBam.bam


Manual

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


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