Hi GATK Users,

Happy Thanksgiving!
Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!

Regards
GATK Staff

using IndelRealigner

guillaume_34guillaume_34 grignonMember
edited July 2016 in Ask the GATK team

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.
(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,

Guillaume

Tagged:

Best Answer

Answers

Sign In or Register to comment.