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.
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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
91824f478e
FASTQ directory is gone
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4986 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 15:16:06 +00:00
3362f0c280
Private mutation simulator and analysis routines for EOMI paper
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4960 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 21:23:29 +00:00
3b76034d50
Namespace changes to avoid conflicts with other packages.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4950 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:33:26 +00:00
ab143c82af
Selects only the project requested via the Oracle command, rather than selecting everything and then subsetting.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4949 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:32:32 +00:00
5583fa179b
Now uses PNGs and a very high downsampling value to more clearly display the information
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4928 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-03 13:57:51 +00:00
dba30c4118
Subsampling of points, for the case where we have enormous numbers of points
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4927 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-03 13:48:11 +00:00
54adbd2581
Added instantaneous rate plotting routine to performance log plotter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4926 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-03 13:33:35 +00:00
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
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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
586d3f05d9
Better cumhist function
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4920 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-02 23:32:20 +00:00
b024b85798
misc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4899 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 20:16:41 +00:00
cc909602c7
Vectorize() pDirectlyPhaseHetPairAtDistanceUsingDepth; deal with minor precision issues
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4890 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-21 17:18:26 +00:00
a829284d84
Return analyzed window sizes as well
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4884 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 17:00:17 +00:00
6310a524d9
Do not abort integration (over het-het distances) on errors, but warn about them
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4855 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 17:20:25 +00:00
b1f0df0047
Handle case where read lengths are longer than fragment size
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4852 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 02:19:55 +00:00
a5e1854b3a
Forgot to pass correct parameters to calcPhasingProbsForWindowDistances()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4851 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 01:58:06 +00:00
2b0dc8625c
Updated RBP theoretical model as per Mark's insights regarding the correct understanding of insert sizes being calculated post-hoc from the distance between read lengths. The correct way to think of it is: 1) There's a fragment of length F. 2) Each of it's two ends are read for L bases. 3) The insert size = i = F - 2 * L, after the fragment's assumed identity is determined by mapping the read mates to a reference sequence. Therefore, the external user-defined distribution is on the FRAGMENT SIZES
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4850 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 01:45:20 +00:00
aea481ae01
Trivial bug fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4848 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 18:29:15 +00:00
46cd227613
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
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4845 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 14:56:12 +00:00
c167c6f9eb
Calculate the phasing probabilities for particular intra-het distances
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4838 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 18:44:59 +00:00
4dbdf7a13d
Added ability to sample from intra-het distance distribution
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4836 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 18:09:03 +00:00
4403b9d276
Added probability bound on phasing paths, which slightly speeds up calculations. It seems that a real speed-up can only be achieved by considering fewer paths by doing some form of caching of sub-problems (e.g., dynamic programming or matrix multiplication, as Mark suggested)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4832 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 23:53:56 +00:00
a6397ed8c3
Default R script now plots sensitivity/specificity curve
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4825 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 16:55:11 +00:00
2bf4fc94f0
Try to use more sampling to get a "correct" estimate of multivariate integral
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4815 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-10 02:58:46 +00:00
c64bf80b57
Added theoretical model of read-backed phasing (RBP)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4814 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-10 01:46:09 +00:00
2ac938fe4e
1)
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Minor fixes to avoid crashes vs CG indel files:
- Add count for complex events, not just insertions and deletions
- Handle correctly cases of large indels falling out of bounds of histogram array: added a count of indels ouf of bounds and avoid exceptions.
2) Cosmetic fix for R script assessing UG calling performance: draw red y=x line on top of Simulated vs Estimated AC to get a better view of under/over-estimation of AC.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4758 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 21:08:25 +00:00
9cca14acc5
Changed VCF subsetting procedure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4742 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-28 00:46:29 +00:00
ecd496cf51
Modifications to reflect changes to gsalib. Smarter about figuring out the names of the filtered parts of the callset.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4739 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-27 23:26:03 +00:00
247f33a553
Prefixed all the functions with gsa. in order to distinguish the methods from other possible methods of the same name in the namespace.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4738 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-27 23:24:42 +00:00
8768e1a240
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
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4728 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 14:59:16 +00:00
d2fc30d188
Added a debugging statement to plot.venn
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4718 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-23 01:19:31 +00:00
d492eb94ad
Actually subsets the resulting table now, like it was supposed to all along.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4696 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:18:23 +00:00
50dbbdb8ab
Retrieves per-sample or per-lane metrics from the SQUID database and populates a dataframe with the results.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4693 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 22:46:07 +00:00
44d0cb6cde
New version of cutting routines for VQSR. Old code removed. Working unit tests. Best practice with testng integration test (everyone look at it). Walker test now allows you to not specify no. input files, if it can infer input counts from MD5s
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4664 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-13 16:19:56 +00:00
4f4eec12dd
Minor improvement
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4659 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 19:30:54 +00:00
760f06cf8c
now prints a nice report, can be invoked from command line
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4641 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-09 19:44:10 +00:00
3c08a1c061
Basic script for assessing simulation sensitivity and specificity
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4638 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-08 21:02:10 +00:00
1d68b28bbd
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).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4584 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-27 19:06:22 +00:00
0508dd0c31
Better reporting -- figured out how to drop unused levels in subset
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4438 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-06 14:31:51 +00:00
24cf6f9e36
Fix to handle situation where there are no filtered variants.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4424 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-04 18:34:01 +00:00
62f5383859
* Added an R package, "gsalib", providing a place to store common, useful, documented R methods. To use this module, you must follow three steps:
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1) Build the module with the following command:
$ ant gsalib
2) Add the module path to your ~/.Rprofile file:
.libPaths("/path/to/Sting/trunk/R/")
3) At the top of each R script that will use the library, include the line:
library(gsalib)
You can now use the package like any other R package. To get high-level documentation, supply the following command to R:
help(gsalib)
The methods contained herein are:
getargs : A method to easily provide arguments to interactive and non-interactive scripts.
Prints out a help message specifying how the script should be run if no arguments
or "-h" is provided. Very helpful when you're writing an R-script piecemeal in
interactive mode, then want to make it a command-line program.
plot.venn : Plots a two-way or three-way proportional Venn diagram.
read.eval : Reads VariantEval output that's formatted in R style.
read.gatkreport : Reads GATKReport output.
gsa.message : Emits a message with the prefix "[gsalib]" to stdout.
gsa.warn : Emits a warning message with the prefix "[gsalib] Warning:" to stdout.
gsa.error : Emits an error message with the prefix "[gsalib] Error: to stdout, calls traceback()
and halts execution.
Documentation on each of these methods can be obtained by typing "help(method_name)" at the R prompt.
* Retired GATKReport.R, as that functionality has now been moved to gsalib.
* Retired gsacommons, as that functionality has been split between gsalib and VariantReport.R.
* Modified VariantReport.R to make use of gsalib. The script now uses the getargs() method to provide the user with some information as to the proper way to run the script. Documentation on how to prepare output is given at http://www.broadinstitute.org/gsa/wiki/index.php/VariantEval .
* Added 'gsalib' target to build.xml file. Running "ant gsalib" will compile this module and place the R-ready package in R/gsalib .
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4416 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-04 00:27:59 +00:00
40b2f62a83
Changed precision on Ti/Tv in venn diagrams
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4413 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-02 05:27:13 +00:00
d0e44b7a8e
Lower precision on Ti/Tv in variant summary matrix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4412 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-02 05:18:48 +00:00
6deb755164
Ti/Tv plots are restricted to a Ti/Tv range of 0.0-4.0. Added column to variant summary specifying the total variant counts (known+novel). Allele spectrum plots now show neutral expectation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4411 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-02 05:15:34 +00:00
1d7e48c4b0
Venn diagrams are now oriented properly when a < b. Added a slide with callset summary table. All plots now show the present-in-a, filtered-in-b metrics. Added title page with project name, author, and timestamp.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4407 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-01 22:17:21 +00:00
fe29c8b09c
Placeholder commit: improvements to VariantReport (now shows stats for variants that are called in one set and filtered in another). Better command-line argument support.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4404 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-01 18:46:53 +00:00
9cf079e1bb
Ready for integration with queue script
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4346 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 19:46:01 +00:00
d6bd1debeb
This is an updated version of the automated data processing report. Each page in the report is a stand alone function, which are linked together with a function which pulls all appropriate data (assuming a standard naming convention) and generates the pdf. This script still need to respond appropriately when it doesn't find the data it needs, database access, and a way of getting some information from sequencing for the tearsheet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4335 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-23 18:08:16 +00:00
b57a0a0310
improvements to the report code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4280 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 00:45:13 +00:00
dfdd0b69a9
Removed unused dependency (it was causing a problem by looking for an X11 connection that didn't necessarily exist).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4244 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-09 19:56:00 +00:00
corin
depristo
kiran
fromer
delangel