..
DataProcessingReport
Pipeline tests will only start from scratch after "ant clean", making it faster to debug downstream issues when re-running "ant pipelinetest -Dpipeline.run=run".
2011-01-29 19:44:03 +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
Reformated backdrop--removed the date
2011-01-26 18:25:59 +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
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
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_indelQuality.R
Change to support plotting of indel quality as a function of covariates - for now, just call different R calling script.
2011-01-22 14:09:23 +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
privateMutations.R
FASTQ directory is gone
2011-01-13 15:16:06 +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
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