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GATK RealignerTargetCreator taking forever! Help

DS89DS89 UKMember
edited August 2013 in Ask the GATK team

I am working on exome capture data for barley (1.3Gbp). I am interested in variant calling to find out SNPs in my sample. I have used SAMTools SNP calling and things get done in ~1 hr whereas GATK (inspite of its several steps to prepare the BAM for variant caller) takes forever. I understand my reference is large and since its an exome capture the targeted region is only 60 Mbp of 1.3Gbp. RealignerTargetCreator is the step it takes forever to locate for sites where indel realignment is required. Do someone have any suggestions to speed it up? Or try any other variant caller? I have tried downsampling my BAM with samtools view -s and that too takes as the log says 8 more days to finish :(

Here is my sample command:

java -Xmx20g -XX:MaxPermSize=40G -jar /software/production/gatk/2.3.9/x86_64/GenomeAnalysisTK.jar -T RealignerTargetCreator -I in.bam -R ref.fa -o out.bam

Thanks, D


  • CarneiroCarneiro Charlestown, MAMember

    if you are only interested in the 60Mb captured region, go ahead and use -L to narrow it down to that region only. This is definitely not recommended for general use though.

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