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Not an answer to your question, but interesting read considering IndelRealigner: https://software.broadinstitute.org/gatk/blog?id=7847
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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
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using GATK IndelRealigner
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!
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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