Recalculate analysis of covariates

= Re-analysis of covariates = Determine the covariates affecting base quality scores in the realigned recalibrated BAM file for the comparison. This is an optional step. Make a temp directory mkdir -p ${tmp_folder}_covar

Running GATK CountCovariates java -Xmx${heap}m -Djava.io.tmpdir\=${tmp_folder}_covar \ -jar $gatk \ -R $REF \ -I $PWDS/${subjectID}.realigned.recal.bam \ -knownSites ${DBSNP} \ -T CountCovariates \ -nt $CPUs \ -cov ReadGroupCovariate \ -cov QualityScoreCovariate \ -cov CycleCovariate \ -cov DinucCovariate \ -recalFile $PWDS/${subjectID}.flt.recal_v2.csv \ -L $ExonFile

Making analyzeCovar_v2 folder to save all related plots mkdir -p $PWDS/analyzeCovar_v2 Generate AnlyzeCovariates Plots java -Xmx${heap}m \ -jar ${gatk_analyzecovar} \ -recalFile $PWDS/${subjectID}.flt.recal_v2.csv \ -outputDir $PWDS/analyzeCovar_v2 \ -ignoreQ 3

< Back to Whole Exome Sequencing Analysis Pipeline