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java.lang.IllegalStateException: This method hasn't been implemented yet for (platform)

vaibhavvskvaibhavvsk Member
edited January 2013 in Ask the GATK team

I'm trying to run CountCovariates and getting the error as :

" java.lang.IllegalStateException: This method hasn't been implemented yet for GAIIx "

I have used following program arguments as given below :

Program Args: -T CountCovariates -R /home/adlab/ngs_data/databases/human_g1k_v37.fasta -I D5_b37_aligned_sorted_realn_DupRm.bam -knownSites:dbsnp,VCF /home/adlab/ngs_data/databases/dbsnp_132.b37.vcf -recalFile D5_b37_aligned_sorted_realn_DupRm_countcovariates.csv -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -standard

To trouble shoot it I found that I have added the read groups in bwa sampe by setting platform info as "GAIIx" as given below and it's root for the error.


What's the exact error in my argument list / read group syntax and What could be the cause of the error ? kindly help.

Post edited by Geraldine_VdAuwera on


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