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

NathanWPanike

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?

Geraldine_VdAuwera

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!