Error: Gatk Countcovariates

Question

[Anjali]

I used 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 hg19.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

<h5>ERROR ------------------------------------------------------------------------------------------</h5> <h5>ERROR A USER ERROR has occurred (version 2.0-23-ge9a19be):</h5> <h5>ERROR The invalid arguments or inputs must be corrected before the GATK can proceed</h5> <h5>ERROR Please do not post this error to the GATK forum</h5> <h5>ERROR</h5> <h5>ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.</h5> <h5>ERROR Visit our website and forum for extensive documentation and answers to</h5> <h5>ERROR commonly asked questions http://www.broadinstitute.org/gatk</h5> <h5>ERROR</h5> <h5>ERROR MESSAGE: Could not find walker with name: CountCovariates</h5>

Can anyone please suggest me what is getting wrong during the process??

Thanks

[Whetting]

It appears that they want you to check the documentation?

Answer 1

[dfornika]

The CountCovariates walker was removed in GATK v2..0 Do you have an older version? It should work fine on the GATK 1.6 series.

If you're determined to use GATK 2.0, then the new walker that replaces CountCovariates is BaseRecalibrator but its functionality may be somewhat different than what you want, so read up on it before using it.