..
DataProcessingReport
Utitlity function to for plotting post-run qc metrics
2011-05-26 20:14:25 +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
Moved scripts to phasing/scripts sub-directory
2011-04-11 15:25:39 +00:00
src /gsalib
Updated tearsheet drop
2011-05-04 16:47:47 +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
Misc changes
2011-02-26 15:35:49 +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
exomePreQC.R
Checkpointing some bugfixes with zero-length version directories and missing
2011-06-22 22:56:01 +00:00
exomeQC.R
Removed nDeletions and nInsertions as independent plots -- just not useful given nIndels and insertions/deletion ratio. Fixed jitter problems with rug plots by removing the rugs entirely. Recovered, and improved, comparative features lost by removing the rug plots by getting viewports to work (trivial) so now per sample metrics and distributions are displayed on the same page!
2011-06-22 13:59:46 +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
Misc changes
2011-02-26 15:35:49 +00:00
plot_OptimizationCurve.R
now plots tranches separately from optimizer
2010-08-10 12:02:52 +00:00
plot_Tranches.R
Removing requirement of providing known track in VQSR for the non-humans. Updating placement of legend on tranche plot.
2011-05-05 20:24:06 +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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