corin 6b5474a00a This updates the script to produce a more tearsheet-like output for sample set statistics. Formatting will be updated for aesthetic improvements. There are also several database options that currently pull out misleading information because of changes in sequencing methodology that will be updated to show correct information. Eventually, plot formatting will be updated as well and additional informative plots will be added. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4988 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-13 15:59:06 +00:00
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DataProcessingReport	This updates the script to produce a more tearsheet-like output for sample set statistics. Formatting will be updated for aesthetic improvements. There are also several database options that currently pull out misleading information because of changes in sequencing methodology that will be updated to show correct information. Eventually, plot formatting will be updated as well and additional informative plots will be added.	2011-01-13 15:59:06 +00:00
VariantRecalibratorReport	…
VariantReport	…
analyzeConcordance	…
phasing	Vectorize() pDirectlyPhaseHetPairAtDistanceUsingDepth; deal with minor precision issues	2010-12-21 17:18:26 +00:00
src/gsalib	Namespace changes to avoid conflicts with other packages.	2011-01-06 15:33:26 +00:00
ADPRpages.R	…
Data.Processing.Report.r	…
GATKRunReport.R	Stabilitity improvements to GATK run report system. R code is now robust. XML parser uses the C backend in python, 10x faster. Added shell script that runs the daily reports, and linked the /humgen/ runme.csh to this script. Script now emails the group the daily PDFs to gsamembers	2010-12-15 14:56:12 +00:00
PlotDepthOfCoverage.R	…
analyzeRodProfile.R	…
assessCallingPerformance.R	…
generateBySamplePlot.R	…
plot_Annotations_BinnedTruthMetrics.R	…
plot_ClusterReport.R	…
plot_GATK_performance_log.R	Now uses PNGs and a very high downsampling value to more clearly display the information	2011-01-03 13:57:51 +00:00
plot_OptimizationCurve.R	…
plot_Tranches.R	…
plot_residualError_OtherCovariate.R	…
plot_residualError_QualityScoreCovariate.R	…
plot_variantROCCurve.R	…
plotting_library.R	…
privateMutations.R	FASTQ directory is gone	2011-01-13 15:16:06 +00:00
tearsheet.r	…
titvFPEst.R	Better cumhist function	2011-01-02 23:32:20 +00:00
whole_exome_bait_selection.R	…