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Author SHA1 Message Date
carneiro 55e5971b3b this is a oneoff script to clean the papuans and test TargetCreator and IndelRealigner with scatter gathering. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5457 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-17 17:09:53 +00:00
rpoplin 9c413fbc9e not useful 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5450 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-15 22:47:55 +00:00
carneiro 42f70d9e07 join all per-lane Bams before doing target realigning and indel cleaning. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5435 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-14 16:11:03 +00:00
depristo d01d4fdeb5 Optimized version of produce beagle tool, along with experimental (hidden) support for combining likelihoods depending on estimate false positive rate. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5430 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-12 02:06:28 +00:00
fromer 0b45de14ed Some minor updates to fully utilize the functionality of reduceByInterval 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5411 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-09 20:38:08 +00:00
depristo bf2e02f472 Generic, easy-to-use variant evaluation Queue script that tests indel and SNP call sets against standard evaluation data sets for sensitivity and specificity 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5391 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-07 18:03:29 +00:00
depristo 5c979633f0 Due to a problem in the way that dynamic type selection works, I've added an explicit (temporary) ability to restrict VE to specific variant types (SNPs, INDELs, etc), so that calculations will work when a site has a SNP in dbSNP but is called as an indel, causing the SNP site to mysteriously disappear from the comp track, a huge problem for validation report. VEU updated to allow both dynamic type (old) and just returning everything in the track. 
Also, created a standard Queue script that calculates a suite of standard indel and SNP assessment results.  Will be the basis for a general evaluation Queue script with standardized data files for SNPs and Indels.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5385 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-06 19:31:12 +00:00
chartl a40a8006b5 Added in unit tests for the statistics calculated by the test runner; and bug-fixes to the calculations; so we have some assurance that the statistics coming out the back-end are correct. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5380 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-06 16:54:02 +00:00
chartl 9ca1dd5d62 Miscellaneous changes: 
- RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it)
 - VCFUtils: grabbing VCF headers given a prefix 
 - MathUtils: Useful functions for calculating statistics on collections of Numbers
 - VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure.
 - Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored
      in the window optionally different from those returned by whatever statistic is run across the window
Added:
 - MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that
    it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation
    for when one of the sample sets is small, and the other large. Unit tests to follow.
 - BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations
 - BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome
 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-03 22:43:36 +00:00
carneiro 0daa65b9ef quick and dirty 'close your eyes' solution to run the papuans over the weekend. Will be properly fixed soon. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5370 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-03 21:42:22 +00:00
chartl 0723b0f44c Generalized association is now working. Output is in a horrific format. Implementation of T-testing. Improvements are to look for classes dynamically (a la VariantEval/VariantAnnotator), beautify output, and do optimizations where they exist. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5341 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-01 01:23:37 +00:00
carneiro c7a51f0de7 fixed 1kg pilot dindel calls vcf file and combined all vcfs into one master dindel file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5335 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-28 19:04:58 +00:00
depristo 146756de79 Class name to reflect actual file name. manySampleUGPerformance now operates on 1000 samples! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5326 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-26 23:36:04 +00:00
chartl b089d35b21 Fix expand intervals to do the right thing: 
- No more duplicate intervals
 - Truncation at intervals that already exist, e.g.

exists:      |--------|           |-------|
new:               |---------|
fixed:                 |-----|

note that weird instances like:

exists:           |-|        |-|                  |-|
new:           |---------------------|
fixed:                          |----|

e.g. you're truncated to the nearest interval on whatever side. In general many behaviors could happen in this instance, this is the one currently implemented.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5323 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-26 04:19:01 +00:00
carneiro fd5d1f9cfc minor cosmetic changes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5322 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-25 21:56:35 +00:00
carneiro 81414a21dd dpp: back to using 4gb memory assuming all is right with IndelRealigner now. 
mdcp: Some class structural changes due to the inclusion of indel calls. ApplyCut now chooses the tranche differently for each dataset.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5319 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-25 19:21:02 +00:00
carneiro 6db3210387 the data processing pipeline needs more memory... 
directory updates in the methods pipeline.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5305 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-24 17:22:58 +00:00
carneiro 897a333aba Methods Development Pipeline now has the option of calling indels with the -indels parameter. Also updated some databases and the new NA12878 HiSeq hg19 that Tim just funneled to us, is updated and called. 
Small fixes on the data processing pipeline


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5304 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-24 17:12:55 +00:00
carneiro 2a48ec1307 now only accepts intervals files if the user specifically requests to report bams at interval only. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5291 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-23 16:49:58 +00:00
carneiro c61dd2f09f data processing pipeline now has on the fly bam indexing (powered by Matt) some new parameters, Indel Cleaning with constrain movement and fixMates is gone. 
setting up methods development pipeline for some cosmetic changes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5277 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-18 23:13:54 +00:00
depristo d97ed3e080 Comments for Mauricio 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5275 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-18 16:58:34 +00:00
carneiro acad3ada06 changed baq to calculate_as_necessary. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5270 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-17 23:50:46 +00:00
carneiro 7f9ca6b28a full data processing pipeline, now deleting intermediate files and performing both phases (per lane and combined) of the processing. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5269 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-17 23:34:00 +00:00
carneiro 497e9ab83b too hasty... cleaning up debug messages ;) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5257 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-17 02:11:03 +00:00
carneiro b4da843c49 now processes either a single bam file or a list of bam files in parallel. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5256 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-17 02:07:22 +00:00
carneiro 50c870cfce Data Processing Pipeline: local indel realignment, mark duplicates and BQSR. Done. 
Pacbio pipeline: now all pacbio bams have baq annotated in so running UG is uber fast.

Methods pipeline: minor cosmetic changes.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5253 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-16 17:22:30 +00:00
carneiro 6d3b878dde data processing pipeline script already does: 
. Local Indel Realignment 
. Mark Duplicates

will do:
. Base Quality Score Recalibration (soon)

it's working with a single BAM for testing, but will work with a list of bam files.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5250 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-15 21:49:05 +00:00
carneiro 87e19a17ae small updates to the variant eval part of the pipeline, some updates to the pacbio specific pipeline. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5244 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-15 16:19:07 +00:00
fromer d6e3f2eba6 Added GC content calculator for CNV data 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5240 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-14 22:29:55 +00:00
carneiro 5f10fffa47 merge intervals now prints a sorted list in the end. 
added the ccs datasets to the pbCalling pipeline.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5233 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-11 20:57:59 +00:00
carneiro 50c2fa3c3a this -1 made ALL the difference in the world. Minor bug fix. 
Regular updates to the pbCalling pipeline.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5232 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-11 19:25:09 +00:00
fromer cdf53188d6 Updated DoC to work with scatter-gather; and, also manually implemented scatter-gather by sample above the scatter-gather by interval. Thansk to Khalid for his support! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5231 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-11 19:14:42 +00:00
carneiro c630701a76 Following Ryan's suggestion, I am moving the Methods Development Calling pipeline to the Core. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5226 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-10 17:36:05 +00:00
carneiro 9c2c5efe35 a modified version of the Methods Development calling pipeline made to work with pacbio data. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5225 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-10 16:06:50 +00:00
fromer 947cc44854 Thanks to Matt for walking me through a proper version of VCF_BAM_utilities! Feel free to add to it, or use it to get the samples in a VCF file, a BAM file, or a collection of BAM files 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5223 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-09 18:08:27 +00:00
kshakir 4d1cca95bb Removed deprecated getDbsnpFile. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5221 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-08 21:12:15 +00:00
carneiro e5cfc6ae74 NA12878 hg19 dataset was included to the methods pipeline. (and I am running it) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5217 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-08 16:17:46 +00:00
fromer 8d0f1b75d5 Added queue/util/BAMutilities Object [with BAM and VCF parsing utilities], which is now used by my qscripts that robustly split runs by sample 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5214 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-07 22:17:29 +00:00
fromer 3c1a026c94 Updated script to properly bin DoC values so that down-sampling corresponds to range of DoC values obtainable 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5208 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-07 16:47:55 +00:00
depristo c4707631e2 MethodsDevelopmentPipeline is now the test bed for large scale AWS_S3 logging. Can be disabled from command line if this is necessary 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5203 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-06 17:03:45 +00:00
fromer 8b8b4fced1 Removed explicit memoryLimit, so that memLimit given on the command-line will NOT be ignored... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5202 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-06 01:55:17 +00:00
depristo fe4aa58d35 Removing unused class 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5197 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-04 22:22:28 +00:00
fromer 4cdc974c5f Preliminary Qscript to run DoC for the purpose of CNV detection 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5194 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-04 21:25:59 +00:00
carneiro 358a400474 made ApplyVariantCut a default part of the pipeline, added the -noCut option if you don't want to use it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5189 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-03 19:29:36 +00:00
carneiro 7af003666d added optional argument -cut to apply the variant cut to the ts recalibrated vcf. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5183 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-03 17:34:40 +00:00
chartl 5398cf620a Bug fixes in the in process function (spoiled by python: was not closing my writers). SortByRef now works somewhat like the perl script does, rather than doing a memory-expensive sort. Adding a QTools qscript which is kinda clunky, and will be used mostly for integration tests of these IPFs, pending some better way to construct argument collections and function accessors at compile-time. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5182 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-03 17:32:46 +00:00
carneiro cf15819db5 updated to work with the new VariantEval. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5176 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-02 17:46:07 +00:00
rpoplin 47357b726e Fixing import GenotypeCalculationModel since it doesn't exist anymore. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5175 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-02 15:39:43 +00:00
fromer 7605f0e6c1 Corrected input/output definitions for Queue 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5173 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-02 07:39:00 +00:00
fromer 3839fd1a25 Updated phasing pipeline to properly read samples from VCF and BAM files 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5172 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-02 07:16:05 +00:00