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

vaibhavvskvaibhavvsk Posts: 6Member
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.

"@RG\tID:Clone-D5\tPL:GAIIx\tLB:LIB-RDT\tSM:UNKNOWN\I:200"

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

Vaibhav Kulkarni Advanced Centre for Treatment Research and Education in Cancer(actrec.gov.in),Mumbai

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