The current GATK version is 3.6-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.

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
Tagged:

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,713 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.

    http://www.broadinstitute.org/gatk/guide/article?id=1186

    Good luck!

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.