Error in CountCovariates as well in BaseRecalibrator

Sakshi

I am using the latest version of GATK, During the Quality score recalibration I found the following error. The code was as follows: java -Xmx4g -jar GenomeAnalysisTK.jar -l INFO -R ~/SCZ_data/ref_hg19/hg19sum_upper.fa --DBSNP dbsnp132.txt -I ../output.marked.realigned.fixed.bam -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile input.recal_data.csv

ERROR MESSAGE: Could not find walker with name: CountCovariates

later i understood that i should use BaseRecalibrator for this new version of GATK, but i am still not sure what to put in the reference file for SNPs with the -knownSites command from where to obtain these vcf files?

java -Xmx4g -jar GenomeAnalysisTK.jar \ -T BaseRecalibrator \ -I my_reads.bam \ -R resources/Homo_sapiens_assembly18.fasta \ -knownSites bundle/hg18/dbsnp_132.hg18.vcf \ -knownSites another/optional/setOfSitesToMask.vcf \ -o recal_data.grp

Can you please suggest me what should be done??

Geraldine_VdAuwera

Please see this FAQ for guidance on choosing known sites: http://gatkforums.broadinstitute.org/discussion/1247/what-should-i-use-as-known-variantssites-for-running-tool-x