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Comments (2)

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.

Comments (4)

Sorry to post such a simple question but I seem to be at my wits end. Base Recalibrator keeps giving me this error:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.0-36-gf5c1c1a):
ERROR
ERROR MESSAGE: The platform (HiSeq2000) associated with read group org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord@32 is not a recognized platform. Implemented options are e.g. illumina, 454, and solid
ERROR ------------------------------------------------------------------------------------------

Why isn't HiSeq2000 recognized as Illumina?