Old pipeline for use with newer GATK is causing me headaches. Can you help?

NathanWPanikeNathanWPanike Member Posts: 0
edited January 2013 in Ask the GATK team

I have a pipeline someone gave me; in it, it runs the following obsolete GATK command:

java -Xms5g -Xmx5g -jar src/GenomeAnalysisTK-1.0.5506/GenomeAnalysisTK.jar -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -R data/ucsc.hg19.fasta --DBSNP data/hg19/snp131.rod -I runs/nwp/run-000/chrUn_gl000228.realn.bam -recalFile runs/nwp/run-000/chrUn_gl000228.recal.csv

How does the following differ from above?

java -Xms5g -Xmx5g -jar src/GenomeAnalysisTK-2.1-8-g5efb575/GenomeAnalysisTK.jar -T BaseRecalibrator -I runs/nwp/run-000/chrUn_gl000228.realn.bam -R data/ucsc.hg19.fasta -knownSites data/dbsnp_135.hg19.vcf -o runs/nwp/run-000/chrUn_gl000228.recal.grp

Then there is another step at this stage of the pipeline:

java -Xms5g -Xmx5g -jar src/GenomeAnalysisTK-1.0.5506/GenomeAnalysisTK.jar -R data/ucsc.hg19.fasta -I runs/nwp/run-000/chrUn_gl000228.realn.bam -o runs/nwp/run-000/chrUn_gl000228.recal.bam -T TableRecalibration -baq RECALCULATE --doNotWriteOriginalQuals -recalFile runs/nwp/run-000/chrUn_gl000228.recal.csv

How does one run this last step map in 2.1-8 version of GATK?

Post edited by Geraldine_VdAuwera on


  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,303 admin

    Hi Nathan,

    You shouldn't be trying to compare old pipelines and new tools directly, because there is not a one-to-one correspondence. You need to take a step back from the commands and understand what are the conceptual steps that these commands perform in the old pipeline. I recommend you use our Best Practices as a guide to figure that out. Then you will be able to use the new tools to perform those steps in a way that follows our Best Practices.


    Good luck!

    Geraldine Van der Auwera, PhD

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