using GATK IndelRealigner

[guillaumers]

Hi,

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. (an igv capture of an ambiguous region that isnt resolved after realignement : https://postimg.org/image/7yuy0hz81/ ). 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

I'm willing to take any ideas!

[tristan dubos]

Hi Guillaume,

The correction appends if there is a better alignment possible, how do you know you should have a different alignment in this position ?

Tristan

[wdecoster]

Not an answer to your question, but interesting read considering IndelRealigner: https://software.broadinstitute.org/gatk/blog?id=7847