quality score recalibration-CountCovariates option

[carolW]

Hi, CountCovariates is not an option for quality score recalibration. Which type of analysis could be used with -T option?

java -jar GenomeAnalysisTK.jar -l INFO -R /home/carolw/NGS/hg19/ucsc.hg19.fasta --DBSNP dbsnp132.txt -I ~/NGS/data/SRR062641.filt.marked.bam.list -T BaseRecalibrator -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -recalFile ~/NGS/data/SRR062641.filt.recal.csv -o ~/NGS/data/SRR062641.filt.marked.qual.bam

ERROR MESSAGE: Walker CountCovariates is no longer available in the GATK; it has been deprecated since version 2.0


Look forward to your reply,

Carol

[geertvandeweyer]

Afaik this Walker is remplaceer by The BQSR Walker.

See: http://www.broadinstitute.org/gatk/g...alibrator.html

Best

Geert