depristo 5539c2d9f3 --performanceLog (-PF) X.dat argument now enabled. Writes out a table (R-friendly) of the performance of the GATK over time, exactly as a more detailed version of the INFO progress meter. R script for useful plotting of the performance of the GATK over time. Will be helpful for upcoming scalability testing and debugging of memory leaks and other incremental performance problems ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4921 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-02 23:34:21 +00:00
..
DataProcessingReport	Takes a list of BAMs, looks up the read group information in the sequencing platform's SQUID database, and computes the tearsheet stats. Also takes the VariantEval output (R format) and outputs the variant stats and some plots for the tearsheet. This script requires the gsalib library to be in the R library path (add the line '.libPaths('/path/to/Sting/R/')' to your ~/.Rprofile).	2010-10-27 19:06:22 +00:00
VariantRecalibratorReport	Removed unused dependency (it was causing a problem by looking for an X11 connection that didn't necessarily exist).	2010-09-09 19:56:00 +00:00
VariantReport	Changed VCF subsetting procedure.	2010-11-28 00:46:29 +00:00
analyzeConcordance	Using bitmap() instead of png() since the former doesn't rely on X11.	2010-02-23 05:31:51 +00:00
phasing	Vectorize() pDirectlyPhaseHetPairAtDistanceUsingDepth; deal with minor precision issues	2010-12-21 17:18:26 +00:00
src/gsalib	Prefixed all the functions with gsa. in order to distinguish the methods from other possible methods of the same name in the namespace.	2010-11-27 23:24:42 +00:00
ADPRpages.R	Ready for integration with queue script	2010-09-24 19:46:01 +00:00
Data.Processing.Report.r	updated version of the DPR. Now produces part of the tearsheet as well as good depth of coverage figures	2010-09-01 15:38:58 +00:00
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	Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics	2010-03-29 13:32:00 +00:00
analyzeRodProfile.R	Useful profiling tool that reads in a single rod and evalutes the time it takes to read the file by byte, by line, into pieces, just the sites of the vcf, and finally the full vcf. Emits a useful table for plotting with the associated R script that can be run like Rscript R/analyzeRodProfile.R table.txt table.pdf titleString	2010-11-24 14:59:16 +00:00
assessCallingPerformance.R	1)	2010-11-30 21:08:25 +00:00
generateBySamplePlot.R	R script for graphing depth of coverage by sample name, and generating a loess curve for each sample's data.	2009-12-10 21:58:01 +00:00
plot_Annotations_BinnedTruthMetrics.R	Can run R scripts on the command line	2010-07-09 00:13:18 +00:00
plot_ClusterReport.R	Can run R scripts on the command line	2010-07-09 00:13:18 +00:00
plot_GATK_performance_log.R	--performanceLog (-PF) X.dat argument now enabled. Writes out a table (R-friendly) of the performance of the GATK over time, exactly as a more detailed version of the INFO progress meter. R script for useful plotting of the performance of the GATK over time. Will be helpful for upcoming scalability testing and debugging of memory leaks and other incremental performance problems	2011-01-02 23:34:21 +00:00
plot_OptimizationCurve.R	now plots tranches separately from optimizer	2010-08-10 12:02:52 +00:00
plot_Tranches.R	Default R script now plots sensitivity/specificity curve	2010-12-13 16:55:11 +00:00
plot_residualError_OtherCovariate.R	Can run R scripts on the command line	2010-07-09 00:13:18 +00:00
plot_residualError_QualityScoreCovariate.R	Can run R scripts on the command line	2010-07-09 00:13:18 +00:00
plot_variantROCCurve.R	Can run R scripts on the command line	2010-07-09 00:13:18 +00:00
plotting_library.R	Can run R scripts on the command line	2010-07-09 00:13:18 +00:00
tearsheet.r	This script produces tearsheet and data processing report figures and tables when given Squid and Firehose produced data	2010-06-18 21:36:29 +00:00
titvFPEst.R	Better cumhist function	2011-01-02 23:32:20 +00:00
whole_exome_bait_selection.R	R script for selecting a variety of baits (using %GC content and normalized coverage) for Nanostring assessment from those used in the Agilent whole exome hybrid selection design.	2009-09-22 18:10:14 +00:00