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