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

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,122Administrator, GATK Developer admin

    See this article for allowed platform values. In your case, replacing GAIIx by Illumina should be the most appropriate.

    Note that you are using an older version of the GATK; for best results we recommend you upgrade to the latest version.

    Geraldine Van der Auwera, PhD

  • vaibhavvskvaibhavvsk Posts: 6Member

    Hey Thanks Geraldine_VdAuwera for the solution, I have read your article regarding the input files and it's well explained. I will replace the older version with newer version.

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

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