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 

HG00100.qplot.pdf