Understanding QPLOT output
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Example QPLOT Output
QPLOT produces the following files:
- *.qplot.R
- *.qplot.stats
See QPLOT output documentation for more details.
QPLOT Tutorial Output
The VerifyBamID output from the GotCloud Tutorial looks like this:
HG00096.qplot.stats
Stats\BAM /home/mktrost/gotcloudTutorialOut/alignment.recal/HG00096.recal.bam /home/mktrost/gotcloudTutorialOut/tmp/alignment.dedup/HG00096.dedup.bam TotalReads(e6) 0.02 0.02 MappingRate(%) 99.66 99.66 MapRate_MQpass(%) 99.66 99.66 TargetMapping(%) 0.00 0.00 ZeroMapQual(%) 0.07 0.07 MapQual<10(%) 0.12 0.12 PairedReads(%) 99.55 99.55 ProperPaired(%) 98.38 98.38 MappedBases(e9) 0.00 0.00 Q20Bases(e9) 0.00 0.00 Q20BasesPct(%) 99.41 97.76 MeanDepth 4.70 4.70 GenomeCover(%) 0.50 0.50 EPS_MSE 445.09 26.27 EPS_Cycle_Mean 27.39 27.39 GCBiasMSE 0.01 0.01 ISize_mode 185 185 ISize_medium 187 187 DupRate(%) 1.39 1.39 QCFailRate(%) 0.00 0.00 BaseComp_A(%) 27.5 27.5 BaseComp_C(%) 22.5 22.5 BaseComp_G(%) 22.5 22.5 BaseComp_T(%) 27.5 27.5 BaseComp_O(%) 0.0 0.0
HG00096.qplot.R
The R file starts with:
NFiles=2; colvec=c(1,2); grid.col='gray'; pchvec=c(1,2); legend.txt=c('HG00096_recal','HG00096_dedup'); lty.vec=c(1); pdf(file="", height=12, width=12);
Update the
pdf(file="", height=12, width=12);
line to be:
pdf(file="HG00096.qplot.R", height=12, width=12);
Then use Rscript to generate the PDF:
Rscript HG00096.qplot.R
HG00096.qplot.pdf
HG00100.qplot.stats
Stats\BAM /home/mktrost/gotcloudTutorialOut/alignment.recal/HG00100.recal.bam /home/mktrost/gotcloudTutorialOut/tmp/alignment.dedup/HG00100.dedup.bam TotalReads(e6) 0.01 0.01 MappingRate(%) 97.13 97.13 MapRate_MQpass(%) 97.13 97.13 TargetMapping(%) 0.00 0.00 ZeroMapQual(%) 0.19 0.19 MapQual<10(%) 0.26 0.26 PairedReads(%) 99.86 99.86 ProperPaired(%) 93.66 93.66 MappedBases(e9) 0.00 0.00 Q20Bases(e9) 0.00 0.00 Q20BasesPct(%) 93.74 95.70 MeanDepth 2.58 2.58 GenomeCover(%) 0.43 0.43 EPS_MSE 477.21 22.19 EPS_Cycle_Mean 23.98 23.98 GCBiasMSE 0.02 0.02 ISize_mode 388 388 ISize_medium 380 380 DupRate(%) 2.43 2.43 QCFailRate(%) 0.00 0.00 BaseComp_A(%) 28.0 28.0 BaseComp_C(%) 22.2 22.2 BaseComp_G(%) 22.1 22.1 BaseComp_T(%) 27.7 27.7 BaseComp_O(%) 0.0 0.0
HG00100.qplot.R
The R file starts with:
NFiles=2; colvec=c(1,2); grid.col='gray'; pchvec=c(1,2); legend.txt=c('HG00100_recal','HG00100_dedup'); lty.vec=c(1); pdf(file="", height=12, width=12);
Update the
pdf(file="", height=12, width=12);
line to be:
pdf(file="HG00100.qplot.R", height=12, width=12);
Then use Rscript to generate the PDF:
Rscript HG00100.qplot.R