3ac5ac066f
Checking in Michael's DoC parameterization script;
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this functionality will eventually be moved into VariantFiltration
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1515 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 15:07:49 +00:00
d804a119dc
script to run the complete pilot2 pipeline: from cleaning to calling to filtering
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[not quite finished though]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1512 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 14:35:55 +00:00
b01ac9de0c
High performance LocusIterator implementation. Now with greatly reduced memory impact and 2x (and more potentially) speed ups of raw locus iteration. General performance improvements to SSG with empirical probs. You can enable high-performance locus iteration with the -LIBS arg. It's still testing but passes validing pileup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1510 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 03:06:25 +00:00
2402dcd4c9
Give usage message if no arguments provided.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1483 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 00:28:43 +00:00
ee05ddde16
Added command line options to make the barcode analysis script executable by end users.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1455 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-24 21:15:09 +00:00
0e7c158949
I've pulled out the functionality of the analyzer into a single python file which doesn't require all of the irrelevant config parameters (which would cause problems for external users). I'll release this and the simple config file to 1KG for use in analyzing recalibration efforts.
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Please note that this is literally my first foray into the wonderful world of python. There could very well be a much more elegant way of releasing the script to external users without having to duplicate the file. If so, anyone out there should (please) feel free to do so in a second release; but, for now, this needs to be online by tomorrow morning.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1404 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-11 02:56:43 +00:00
afccbc44ec
Script that performs all the processing steps from raw Illumina reads through to analysis of barcoding and hybrid selection efficience as documented in the GATK tutorial; can automatically run all steps in series on the farm.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1354 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 00:22:53 +00:00
eb4b9a743a
Script that runs most of the steps involved in validating the CoverageEval system that predicts performance for given depth of sequencing coverage across a genome.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1353 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 00:18:45 +00:00
efd0fd1f0a
Short python script that takes paired-end BAMs and aligns them with BWA. Referenced in GSA wiki tutorial
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1351 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 00:04:10 +00:00
1c648a2d5f
Skip compiled python files (*.pyc) in svn status output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1346 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 21:45:23 +00:00
d665d9714f
By default now writes output to JOBID.lsf.output instead of going to email -- based on recommendations from the cancer group
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1325 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-28 13:18:58 +00:00
00f9bcd6d1
CoverageEval.py tool right before some major changes to the core of the code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1293 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-22 16:58:23 +00:00
702cdd087f
Actually listens to justPrint now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1253 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 16:52:46 +00:00
c25f84a01c
Regression: we lost our hack to work around BAM files with index problems (affects BAM files created before 23 Apr 2009 and traversed by interval). Added the hack back in, along with a much more explicit comment about why its there.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1248 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 14:41:37 +00:00
84d407ff3f
Fixing odd merge problem with VariantEval -- better cluster analysis (no cumsum), rodVariant is now an AllelicVariant
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1239 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 18:53:27 +00:00
c8fcecbc6f
Added ParseDCCSequenceData.py to repository and made changes that allow an analysis of quantity of sequence data by platform and project, moved table / record system to a new module called FlatFileTable.py and built that into ParseDCCSequenceData and CoverageEval.py; changed lod threshold in CoverageEvalWalker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1201 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 22:04:26 +00:00
d3daecfc4d
Added unit tests for function in ListUtils to randomly sample lists with replacement, updated AlleleFrequencyEstimate to provide a callType of HomRef, HetSNP, HomSNP, update indices in CoverageEval.py, and made a lot of changes to CoverageWalker biggest one being that it directly calls SingleSampleGenotyper instead of implementing some parts of SSG itself.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1189 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 02:05:40 +00:00
f5b00c20d0
Updated python files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1182 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 14:15:39 +00:00
dcb8892568
Lot of code for coverage evaluation tools including first version of python script to evaluate the downsampled SSG callls made and the java code to make all the calls at Hapmap chip sites at various downsampling levels; ListUtils contains functions for randomnly subsetting lists (with replacement) which are useful for subsetting the same elements in both the reads and the offsets lists of a LocusWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1162 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-03 08:07:02 +00:00
5289230eb8
Version 0.2.1 (released) of the TableRecalibrator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:50:55 +00:00
caf5aef0f8
Much improved python analysis routines, as well as easier / more correct merging utility. Better R scripts, which now close recalibration data by the confidence of the quality score itself
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1081 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 01:12:35 +00:00
c9e6cb72e1
Major improvements to python analysis code -- now computes a host of statistics about quality scores from the recal_data.csv file emitted by countcovariates. Includes average Q scores, medians, modes, stdev, coefficients of variation, RSME, and % bases > q10, q20, q30. Can finally quantify and compare the improvement of quality score recalibration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1064 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-20 19:50:37 +00:00
9e26550b0d
Apprach v2. Added python analysis script, so java no longer must be used to analyses quality score data. About to refactor out lots of unneeded code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1063 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-20 16:00:23 +00:00
8ac40e8e2d
Updated version of the recalibration tool
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1060 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 17:45:47 +00:00
17a5b50ea4
Script that aligns paired-end BAMs using BWA.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1042 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 18:14:58 +00:00
260fd0dc45
Trivial change
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1000 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 19:11:28 +00:00
fb7ba47fff
Now does really neightbor distance calculation, as well as true snp cluster counting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@998 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 16:29:26 +00:00
1fb241a8b8
Now supports resume and dry runningRecalQual.py
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@996 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 23:31:59 +00:00
5440dd13df
Preparation for point release of read calibrator: no artificial heap size limit, no duplicate dbsnp records.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@986 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 18:39:33 +00:00
e77dfe9983
Allow script to be easily modified to support different platforms.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@955 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 16:06:57 +00:00
7fa84ea157
10x speedup of recalibration walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@954 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 15:39:40 +00:00
5fa3f7ed3a
Added absolute path bug fix for Mark.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@949 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 02:25:17 +00:00
127c321d0a
Cut over to 1kG version of fasta / reference. Updated doc with latest version of tool summary.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@940 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 21:11:44 +00:00
596773e6c6
Cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@931 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-07 20:25:08 +00:00
e6aa058ec4
Tighten up error handling a bit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@920 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-06 03:40:50 +00:00
819862e04e
major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@918 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 23:34:37 +00:00
050d55cdb0
Basic graph support for testing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@916 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 21:04:01 +00:00
2035d7dfd3
Revert some debug code in RecalQual.py. Make LogisticRegression easier to Ctrl-C out of.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@904 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 01:53:48 +00:00
61ae00c7bf
Lots of cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@903 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 01:26:10 +00:00
9689bb3331
Very early draft of script integrating the covariant counting / logistic regression. Deleted some unused code and spurious debug info.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@902 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 22:52:11 +00:00
40bc4ae39a
The building blocks for segmenting covariate counting data by read group.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@899 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 19:55:24 +00:00
67112c79a1
More robust individual genotypes to population script
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@893 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 00:12:31 +00:00
7755476d36
Updated coverter to reflect change in contig ordering in Geli files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@888 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-03 10:05:28 +00:00
080af519cb
Added R script and uncommented a line in recal_qual.py
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@886 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-03 03:15:45 +00:00
b2eb724456
First commit of recalibration master control script for recalibrating quality scores.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@885 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-03 02:17:10 +00:00
3998085e4b
more and better python scripts for dealing with calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@881 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 20:37:19 +00:00
587d07da00
Merged functionality of two python scripts into LogRegression.py, some clarity updates to covariate and regression java files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@876 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 16:55:05 +00:00
ae2eddec2d
Improving, yet again, the merging of bam files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@874 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 13:31:12 +00:00
543c68cdd8
First version of individual geli files to population SNPS
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@865 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-31 15:29:10 +00:00
6adef28b97
Now supports automatic merging by population
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@864 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-31 15:28:44 +00:00
ebanks
depristo
andrewk
hanna