Analysis of covariates

= Analysis of covariates = Determine the covariates affecting base quality scores in the BAM file. 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 \ -l INFO \ -I $PWDS/${subjectID}.realigned.srt.bam \ -knownSites $DBSNP \ -T CountCovariates \ -nt $CPUs \ -cov ReadGroupCovariate \ -cov QualityScoreCovariate \ -cov CycleCovariate \ -cov DinucCovariate \ -recalFile $PWDS/${subjectID}.flt.recal_v1.csv \ -L $ExonFile

Making analyzeCovar folder to save all related plots mkdir -p $PWDS/analyzeCovar_v1

Generate AnlyzeCovariates Plots java -Xmx${heap}m -Djava.io.tmpdir\=${tmp_folder}_covar \ -jar ${gatk_analyzecovar} \ -recalFile $PWDS/${subjectID}.flt.recal_v1.csv \ -outputDir $PWDS/analyzeCovar_v1 \ -ignoreQ 3

Remove the temp directory rm -rf ${tmp_folder}_covar

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