Question: using GATK IndelRealigner
gravatar for guillaume.rbt
2.8 years ago by
guillaume.rbt560 wrote:


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 : ). 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!

alignment • 1.4k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by guillaume.rbt560

Have you considered using the haplotype caller instead, so you can skip indel realignment?

Anyway, the IndelRealigner isn't perfect and misses the occasional site that one might like it to realign. What is the sequence of the insertions?

ADD REPLYlink written 2.8 years ago by Devon Ryan90k

Thanks for the answer. Indeed using Haplotype caller should solve my problem. But I wanted to use indelRealigner for using other indel detection tools. I understand that it isn’t perfect, and I should filter my results to check for false positives.

(the insertion sequence is GT, I think the "real" polymorphism is the 3 substitutions TTG, but sometimes bwa chose to put a deletion followed by an insertion)

ADD REPLYlink written 2.8 years ago by guillaume.rbt560

Hello guillaume.rbt!

It appears that your post has been cross-posted to another site:

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 2.8 years ago by WouterDeCoster39k
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