Sorry to post such a simple question but I seem to be at my wits end. Base Recalibrator keeps giving me this error:
Why isn't HiSeq2000 recognized as Illumina?
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.