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
594fb4a547
More plots in report
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4225 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-08 02:56:51 +00:00
19e22cfa87
Fixed a bug where the script looked for the wrong column name. Also, all results are now returned in a single plot.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4216 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-06 14:19:57 +00:00
0c54bf4195
Better reporting and now with a special mode for listing exceptions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4183 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 16:19:51 +00:00
cdad243645
updated version of the DPR. Now produces part of the tearsheet as well as good depth of coverage figures
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4182 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 15:38:58 +00:00
fc5caa98a5
Improved reporting now with metrics by day/week/etc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4180 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 02:43:13 +00:00
8683087756
Suppl. tools for working with and displaying GATK run reports
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4176 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 20:32:22 +00:00
e14a347e2e
Now prints cluster report to a single PDF, rather than a dozen different PDFs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4164 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-29 18:58:39 +00:00
fd19c63aaf
A data structure that allows data to be collected over the course of a walker's computation, then have that data written to a PrintStream such that it's human-readable, AWK-able, and R-friendly (given that you load it using the GATKReport loader module).
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This object designed to be both the structure that holds data during the execution of the walker, as well as the object that properly formats and emits the data so that it can be easily loaded into R. In the end, you get a table that looks like this:
##:GATKReport.v0.1 ErrorRatePerCycle : The error rate per sequenced position in the reads
cycle errorrate.61PA8.7 qualavg.61PA8.7
0 0.007451835696110506 25.474613284804366
1 0.002362777171937477 29.844949954504095
2 9.087604507451836E-4 32.87590975254731
3 5.452562704471102E-4 34.498999090081895
4 9.087604507451836E-4 35.14831665150137
5 5.452562704471102E-4 36.07223435225619
6 5.452562704471102E-4 36.1217248908297
7 5.452562704471102E-4 36.1910480349345
8 5.452562704471102E-4 36.00345705967977
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A GATKReport object can hold multiple tables, and the write() method will emit all tables in succession. Each table starts with its own ##:GATKReport.v0.1 table header, so each table can stand alone. This allows for tables to be mixed and matched in a single file, or for the output from different walkers to be combined into a single file with no ill effect.
The display property of individual columns can be turned off. This is useful when a column is used to store intermediate results, necesary for the computation of some later value, but the contents of the intermediate column itself are not required in the final output file.
Finally, the GATKReportTable allows for some simple, mathematical, element-wise and column-wise operations. For instance, two whole columns can be divided, the results of the operation being stored in a third column. This mimics the most basic of R operations, where whole vectors can be added, subtracted, multiplied or divided without requiring the developer to explicitly write a loop.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4159 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-29 05:39:24 +00:00
8931a63588
updated a whole bunch of column names to work like i want them to and added more informative figures for DOC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4131 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-26 18:19:09 +00:00
fba71e3c15
Placeholder commit. Implements a loader for a new multi-part GATK reporting format. See what it looks like at /home/radon01/kiran/scr1/projects/NewVariantEvalOutput/results/v1/tableexample.txt . Still need to address the issue where numeric columns are being interpreted as a vector of strings, not numbers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4115 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 18:48:44 +00:00
8054b6b295
Changing a name of a column for variantevals output for easier reading by R--let me know if this needs to be updated elsewhere; it's just a space to an underscore.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4062 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 19:18:16 +00:00
ede87a03c2
Nicer plotting routine for tranches. Add a third arg to suppress the legend.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4049 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-17 19:20:58 +00:00
e0abb73fd7
plot now assumes 1 / 1000 is the min error rate, not 1/100
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4010 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-11 14:48:22 +00:00
6037443e55
Handle interactive and non-interactive modes more elegantly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4009 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-11 02:38:53 +00:00
a7409df1a6
Be more robust to missing or empty files in VariantEval output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4008 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-11 02:22:50 +00:00
67063deb16
Removed coloring by mixture weight. Each cluster gets a distinct color, and the legend indicates which cluster has which id and its weight
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4001 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 14:28:24 +00:00
672bee295c
now plots tranches separately from optimizer
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4000 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 12:02:52 +00:00
41fee2d75e
Publication tranches report is now the default output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3967 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-07 13:58:59 +00:00
f4ffef4479
Default max variants is now 5000
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3966 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-07 13:58:32 +00:00
b63d64bbbc
Beautiful labels, better choice of dimension ranges. Supports fast loading of just first N records for testing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3964 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-06 23:17:32 +00:00
d3bebe0f2c
Reasonable comment
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3963 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-06 22:03:55 +00:00
bb5dfd7e5e
Slightly nicer plotting; not yet complete
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3961 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-06 20:01:31 +00:00
70f492a6e8
Prints out trivial debugging info
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3957 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-06 13:24:21 +00:00
1a36cb9296
Can now set the maximum number of variants to see in a cluster plot (useful when you don't need to see a billion points to get an idea of what's going on. Limit applies to known and novel variants separately.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3937 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 18:45:24 +00:00
bd27287fe7
An R module that takes in a Variant Recalibration cluster file (file with '@!CLUSTER' lines in it), a tabularized VCF, and optionally a set of loci that should be examined more carefully, and emits a tremendous number of plots. For every annotation used in clustering, the distributions and pair-wise comparison (with ellipses denoting the 2-sigma cluster boundaries) are shown. Each cluster is shaded with a color proportional to its mixture coefficient.
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To use this module, you'll first have to take your VCF and create an R-readable table out of it with the following command:
python /path/to/Sting/trunk/python/vcf2table.py -f CHROM,POS,ID,AC,AF,AN,DB,DP,HRun,MQ,MQ0,MyHaplotypeScore,QD,SB my.vcf > my.vcf.table
Then, simply invoke this module with the command:
Rscript /path/to/Sting/trunk/R/VariantRecalibratorReport/VariantRecalibratorReport.R /path/to/output/prefix /path/to/my/my.clusters /path/to/my.vcf.table [/path/to/my.suspicious.loci]
This will create a number of plots all with the prefix "/path/to/output/prefix". For instance, if you used QD, SB, HRun, and MyHaplotypeScore annotations during clustering, you should see output like this:
/path/to/output/prefix.anndist.HRun.pdf
/path/to/output/prefix.anndist.MyHaplotypeScore.pdf
/path/to/output/prefix.anndist.QD.pdf
/path/to/output/prefix.anndist.SB.pdf
/path/to/output/prefix.cluster.HRun_vs_MyHaplotypeScore.pdf
/path/to/output/prefix.cluster.HRun_vs_QD.pdf
/path/to/output/prefix.cluster.HRun_vs_SB.pdf
/path/to/output/prefix.cluster.MyHaplotypeScore_vs_HRun.pdf
/path/to/output/prefix.cluster.MyHaplotypeScore_vs_QD.pdf
/path/to/output/prefix.cluster.MyHaplotypeScore_vs_SB.pdf
/path/to/output/prefix.cluster.QD_vs_HRun.pdf
/path/to/output/prefix.cluster.QD_vs_MyHaplotypeScore.pdf
/path/to/output/prefix.cluster.QD_vs_SB.pdf
/path/to/output/prefix.cluster.SB_vs_HRun.pdf
/path/to/output/prefix.cluster.SB_vs_MyHaplotypeScore.pdf
/path/to/output/prefix.cluster.SB_vs_QD.pdf
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3936 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 18:35:14 +00:00
b990a22bac
A very nice way of automatically plotting the results of a VariantEval run. All of the hard work is actually in the common R repository, gsacommons.R, including methods for creating a Venn diagram. It also provides a mechanism for the output of a VariantEval run to be loaded into a single list object.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3828 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-19 12:38:26 +00:00
6ffcaa0afe
Can run R scripts on the command line
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3750 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-09 00:13:18 +00:00
66931d433c
useful routines for R
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3685 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 16:38:49 +00:00
bcab0eba01
This replaces tearsheet.r, neatens up graphics, and allows the script to be used in R's interactive environment
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3625 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 01:02:58 +00:00
ae88630d52
This script produces tearsheet and data processing report figures and tables when given Squid and Firehose produced data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3594 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 21:36:29 +00:00
a2c266bda3
This script accpets file paths to analysis metrics tables and produces tearsheet data and data processing report graphs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3585 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 13:02:25 +00:00
266a47d83d
This file automaticially generates data and graphics for tearsheets and data processing reports
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3551 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 18:39:23 +00:00
290771a8c2
Automatic cutting of recalibrated variant calls using ApplyVariantCuts. VariantRecalibrator produces the tranches plot alongside the optimization curve. Specify the levels using -tranche 1.0 -tranche 5.0 etc
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3472 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 15:03:00 +00:00
33a9549896
Variant Optimizer accepts a dbSNP rod arugment to use in determining known/novel status as opposed to using the rsID in the vcf record. VO generates plots of annotation values used in clustering broken out by knowns and novels. Useful for showing which annotations are approximately Gaussian.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3332 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-09 16:48:07 +00:00
dc802aa26f
Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3090 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 13:32:00 +00:00
06a212e612
Adding VariantConcordanceROCCurveWalker to create ROC curves comparing concordance between optimized call sets and validation truth sets in VCF format in order to evaluate performance of variant optimizer independently of achieving a particular novel ti/tv ratio. Added option to ignore only the specified filters in the input call sets via --ignore_filter <String>. Added option to provide a prior estimate of error for known snps via --known_prior <qual>. The het and hom calls are clustered independently. Infrastructure in place to use titv of known snps to inform p(true) of novel snps. Tweaked protection against overfitting based on suggestions from several people. Minor edits to AnalyzeAnnotations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3071 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-24 19:43:10 +00:00
c78fc23ec5
Minor updates to output of variant optimizer.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3031 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-18 12:46:47 +00:00
58a31bab6a
Variant optimizer now outputs VCF files via ApplyVariantClustersWalker. Documentation to be added to the wiki. It is ready to be used by other people but only with great caution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3028 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-17 20:41:42 +00:00
933823c8bc
Removed the StingException when mkdir fails for Sendu in AnalyzeCovariates. Incremental updates to VariantOptimizer.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3013 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-16 19:45:02 +00:00
ee68e38e02
Eliminate the shell items, as FH will be calling this with /broad/tools/apps/R-2.72/bin/Rscript
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2968 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 20:15:21 +00:00
aa7191353a
PlotDepthOfCoverage now produces a set of useful QC plots. Currently a first-draft, and it is unclear how the visualization will scale with increasing sample size and/or depth.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2962 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 16:42:35 +00:00
81ffb8243d
Waypoint commit of plotting R script for Depth Of Coverage/Coverage Statistics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2958 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-08 21:42:51 +00:00
36129e01e4
Using bitmap() instead of png() since the former doesn't rely on X11.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2873 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-23 05:31:51 +00:00
3738b76320
Added a playground concordance analyzer for summarizing VariantEval across a group.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2867 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-22 20:28:52 +00:00
f02e94ab6f
Eliminate the rescale factor -- heatmap automatically normalizes the data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2845 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-16 16:34:33 +00:00
37fa1bf0cc
Added heatmap function
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2843 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-16 15:12:54 +00:00
951b7a2433
First of what will be an increasingly useful set of tools, compiled into one command-line runnable library -- the goal is to have one plotting library that's callable because of limitations on the number of files you can package with a GenePattern module.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2841 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-15 16:51:47 +00:00
233a652161
Making the dotted quartile lines more clear.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2772 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-03 22:23:09 +00:00
64fc76e4bf
Added an option to AnalyzeCovariates to set the max value of the histograms to make them easier to directly compare.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2753 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-31 23:13:57 +00:00
16da5011c0
Added a new option for indicating the mean number of variants on the AnalyzeAnnotations plots. This way one can say, for example, filtering at this point will keep 75 percent of all the variants.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2744 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-29 21:58:31 +00:00
c6cc844e55
Added -name argument to AnalyzeAnnotations that allows one to specify the name of the annotation to be used on the plots. Instead of seeing AB and DP, one can add -name AB,AlleleBalance -name DP,Depth
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2742 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-29 20:48:53 +00:00
4f29a1d4f6
AnalyzeAnnotations now plots true positive rate instead of percentage of variants found in the truth set. Committing GCContentCovariate to help people experiment with correcting the pilot3/Kristian base calling error mode in slx.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2740 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-29 20:01:56 +00:00
79c4cc1db7
AnalyzeAnnotations now breaks out titv by calls in hapmap and also plots true positive rates. Any RODs passed in whose name starts with 'truth' is considered to be the truth set.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2726 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-28 21:41:23 +00:00
b8ae083d1b
AnalyzeAnnotations creates a plot of dbsnp rate as a function of the annotations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2711 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 21:08:33 +00:00
fc4285f9fd
AnalyzeAnnotations seems to be popular so I've rewritten the guts to be easier to extend and maintain.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2707 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 19:30:31 +00:00
4bcdab580c
--output_dir has been changed to --output_prefix to give the user more control over the names of the resulting mass of files in AnalyzeAnnotations. The fontsize of the axes is increased. Cumulative filtering plots are removed since the binned filtering plots are much more useful.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2700 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 04:50:54 +00:00
24d4082925
AnalyzeAnnotations can now process only variants that are found in samples that match the -sampleName argument. X-axis of plots no longer use annoying scientific notation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2684 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 20:52:11 +00:00
2b51cf18f0
AnalyzeAnnotations now outputs plots with log x-axis in addition to standard x-axis so things like DP and MQ0 are easier to see. AnalyzeAnnotations now skips over all annotations that aren't floating point values. Recalibrator now warns users if PL tags are missing and so therefore it is reverting to illumina.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2681 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 19:39:18 +00:00
a11503819a
AnalyzeAnnotations now breaks out its TiTv plots into novel SNPs, dbSNP sites, and combined.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2659 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 19:00:23 +00:00
d9df72e1b5
AnalyzeAnnotations now bins variants per each annotation and outputs plots of TiTv ratio as a function of the annotation's value.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2654 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 21:15:11 +00:00
ba19afd529
Draft version of AnalyzeAnnotations which creates plots of cumulative TiTv ratio versus filter value per each annotation in the input VCF rod. Minor cleanup of recalibration walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2623 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-18 20:47:10 +00:00
7f97041875
Update to AnalyzeCovariates to make the histogram of PairedReadOrder look a little nicer
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2575 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 20:26:31 +00:00
cea544871d
Fixed an issue with recalibrating original quality scores above Q40. There is a new option -maxQ which sets the maximum quality score possible for when a RecalDatum tries to compute its quality score from the mismatch rate. The same option was added to AnalyzeCovariates to help with plotting q scores above Q40. Added an integration test which makes use of this new -maxQ option.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2534 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 13:50:30 +00:00
562db45fa5
Sites that were marked NO_DINUC no longer get dinuc-corrected but are still recalibrated using the other available covariates. Solid cycle is now the same as Illumina cycle pending an analysis that looks at the effect of PrimerRoundCovariate. Solid color space methods cleaned up to reduce number of calls to read.getAttribute(). Polished NHashMap sort method in preparation for move to core/utils. Added additional plots in AnalyzeCovariates to look at reported quality as a function of the covariate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2451 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 20:19:37 +00:00
1ae333a1c1
R script for graphing depth of coverage by sample name, and generating a loess curve for each sample's data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2317 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 21:58:01 +00:00
088363ce42
Added entropy calculation to histogram of quality scores
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2316 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 21:57:35 +00:00
12ec154f01
Make the AnalyzeCovariate plots look a little nicer when there are a small number of data points
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2298 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 21:22:40 +00:00
855face681
Histogram of covariate values now goes from 0 to max value which makes it look nicer in most cases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2259 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 14:44:03 +00:00
985daec76e
Fixed problem with integer overflow in R scripts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2258 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 14:24:49 +00:00
fromer
depristo
delangel
kiran
corin
rpoplin
chartl
kshakir
aaron