The current GATK version is 3.7-0
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!

Get notifications!


You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Picard 2.9.4 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

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

NathanWPanikeNathanWPanike Member
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 Cambridge, MAMember, Administrator, Broadie

    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!

Sign In or Register to comment.