Genome Variant Analysis


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

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