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I have some difficulties using IndelRealigner on my data.
After comparing bam files before and after realignement process I find some regions where a correction should have occured.
(enclosed an igv capture of an ambiguous region that isnt resolved after realignement).
Is it normal that all my indels "problems" are not solved? And are there parameters to adjust to solve them?
Have I made mistakes running the commands?
(here are my command lines )
java -Xmx12000m -jar ~/Soft/GATK/GenomeAnalysisTK.jar -T RealignerTargetCreator -nt 15 -R ~/igv/genomes/genome.fa -I sample.bam -o temp.indel.intervals
java -Xmx12000m -jar ~/Soft/GATK/GenomeAnalysisTK.jar -T IndelRealigner -R ~/genome.fa -I sample.bam -targetIntervals temp.indel.intervals -o sample_realigned.bam
Thanks for your help,