d92055d1f9
Checkpointing some bugfixes with zero-length version directories and missing
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Picard metrics files before the push back into svn.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6069 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:56:01 +00:00
3d27e5eb98
Default operating parameters in addition to the parameterized Rscript version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6067 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:55:53 +00:00
c956e154a0
Kill silly plots.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6063 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:55:39 +00:00
28d8b28bdf
Density plots.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6061 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:55:33 +00:00
3392c67e0f
Support for command-line arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6055 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:55:05 +00:00
d9973d3da7
Adding in a template for many other plots based on Mark's initial list of metrics.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6054 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:55:02 +00:00
237f73c1b1
Initial fingerprint boxplot for exome PreQC metrics.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6053 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:54:59 +00:00
9b54239f37
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!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6026 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 13:59:46 +00:00
a37e9bdbd4
Now produces an expanded table at the start, as well
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6017 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-20 13:45:08 +00:00
907018768c
Now uses AC directly from eval, not via AF, internally for AC vs. X plotting. Requires at least 1 SNP to include a site in TiTv plotting or snp/indel ratio. Uses .byAC not .byAF eval file now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6014 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-19 03:05:17 +00:00
285da580f3
Now with dbSNP rate
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6010 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-17 13:21:40 +00:00
9254faa27e
Added density plots by sample for each metric. New command line argument ordering. No longer requires the per-sample.tsv suppl. data -- will conditionally load if available
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6003 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-16 12:46:29 +00:00
ce4e8d2093
A few comments / todos.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6001 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-15 13:09:09 +00:00
6f7c4d1142
Removing exomePostQC.R
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5996 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 16:10:34 +00:00
85e20be7b7
Renamed. More general
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5989 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 20:50:56 +00:00
a837a49328
Minor fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5988 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 20:50:34 +00:00
14a358e5e8
Oops, forgot one tiny thing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5981 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 17:12:42 +00:00
165befd38a
V1 of the post processing QC plotting scala script and R function. The scala script runs VariantEval on a VCF file, and computes QC metrics. The R script generates the report. Will discuss usage with data processing group. Ryan -- please add your additional plotting routines to this script, as you see fit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5980 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 17:06:42 +00:00
a561d3adc7
Utitlity function to for plotting post-run qc metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5885 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 20:14:25 +00:00
fccd5517a0
Generates post run QC plots with by sample metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5884 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 20:13:59 +00:00
59495c7f03
Updated tearsheet function utility
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5883 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 19:58:57 +00:00
8a57c52005
Produces a more throurough tearsheet with detailed metrics and information
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5882 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 19:57:49 +00:00
1e2892a35d
Preliminary QC script in R, which checks coverage, fingerprints, library duplication, total SNPs, dbSNP%, and availability of sample data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5881 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 19:57:00 +00:00
b94d8dae17
Removing requirement of providing known track in VQSR for the non-humans. Updating placement of legend on tranche plot.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5773 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-05 20:24:06 +00:00
b4654b0f47
Status messages to user added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5763 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 20:10:47 +00:00
bcc688c1e9
small formatting change
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5762 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 20:01:20 +00:00
1410327901
Cmd line argument reference fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5761 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 20:00:14 +00:00
3e8fc71743
Missing parenthesis for database access commands added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5755 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 16:59:17 +00:00
23efd66d31
Updated Tearsheet with by sample QC metrics, bugfix for misnamed variables
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5754 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 16:57:48 +00:00
72a07e4553
Updated Tearsheet with by sample QC metrics, bugfix for misnamed variables
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5753 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 16:54:05 +00:00
2e1c09c03b
Updated tearsheet drop
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5752 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 16:47:47 +00:00
f386cad58c
Updated Tearsheet with by sample QC metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5751 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 16:47:26 +00:00
5bade81c6d
Adding tranche plot generation back to VQSR
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5736 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 19:26:26 +00:00
f76e2791a9
Update to work with latest eval format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5720 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 13:44:50 +00:00
139ae79d9e
Update to work with latest eval format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5719 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 13:21:23 +00:00
004f5295ea
Moved scripts to phasing/scripts sub-directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5612 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-11 15:25:39 +00:00
822b4d66ce
FOR KIRAN: Adding R scripts and functions that perform theoretical calculations of phasing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5611 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-11 14:18:30 +00:00
aaecc271e8
Misc changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5324 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-26 15:35:49 +00:00
356eb264ab
Now says FNR, not FDR. We really need to clean up VQSR
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5243 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-15 12:28:09 +00:00
9fc45e1234
Use the yaml as an arguemtn to get out squid numbers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5186 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 18:32:05 +00:00
027c91871f
Commenting out something I meant to leave commented out
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5163 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 15:47:52 +00:00
393df46055
updates to handle only reporting on a specific SVN revision. Updated the R script to show the domain name of the runner, now that S3 logging is working
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5157 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 12:02:12 +00:00
1753f9d864
"Properly handles multiplexed and non multiplex lane data from the picard database."
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5146 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 21:14:32 +00:00
23578b7402
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".
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Updated the FCP, the test, and the ADPR to handle an issue with the ADPR locating the yaml generated by the FCPTest.
Does not solve the ADPR error: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5126 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-29 19:44:03 +00:00
afeb0f63c3
Further, smarter modifications to R script for correctly accessing database data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5124 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-29 03:32:20 +00:00
4f2882c546
Fixing the way that lanes are pulled into from the database so that multiplexed lanes are handled and older sequence data ids are properly handled.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5123 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-29 02:40:10 +00:00
1d8412d652
Updating a few graphical parameters and making sure everything fits together
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5111 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 18:44:23 +00:00
88ea60b864
Updates formatting and combines plots into the tearsheet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5109 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 17:45:23 +00:00
73e2942c62
Reformated backdrop--removed the date
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5086 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 18:25:59 +00:00
b22f82d5dd
Minor formatting udpates to deal with long bait names, multiple sequencer types, and date formatting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5072 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-25 19:02:40 +00:00
droazen
depristo
rpoplin
corin
fromer
kshakir