We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

The requested covariate type (DinucCovariate) isn't a valid covariate option

yuemingdingyuemingding Member
edited August 2012 in Ask the GATK team

Hi I ran the following command line:
java -Xmx4g -jar GenomeAnalysisTK.jar -T BaseRecalibrator -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -I sample.bam -R ucsc.hg19.fasta -knownSites dbsnp_135.hg19.vcf -o recal_data.grp

But I got the following error:

ERROR MESSAGE: Invalid command line: The requested covariate type (DinucCovariate) isn't a valid covariate option. Use --list to see possible covariates.

The GATK I used is v2.0-39-gd091f72, Compiled 2012/08/10 15:55:35. It looks like there is no DinucCovariate covariates available for this new GATK. I tried to get the list of possible covariates by running the following command line:
java -Xmx4g -jar GenomeAnalysisTK.jar -T BaseRecalibrator --list

But it didn't work (I didn't find the list).

Could you please tell me if DinucCovariate covariates is not available in new GATK? How could I get the list of possible covariates?

Thanks!

Best Answer

  • ebanksebanks Broad Institute ✭✭✭✭
    Accepted Answer

    You need a full command-line. The User Error message that you get from running these commands should tell you exactly what pieces you are missing.

Answers

Sign In or Register to comment.