1a5d296737
ReplaceReadGroups. Fixes BAM files without read group info. MissingReadGroup points people to this tool now. Please point users on the forum to this tool now. Will migrate to Picard.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5284 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-21 14:02:41 +00:00
ef2f6d90d2
VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4684 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 22:19:22 +00:00
ac52b64b77
correct test data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4665 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-13 22:17:38 +00:00
c5f8c4dd0d
VariantEval test for tranches file, plus cutting over VE to use the generic Tranches framework
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4656 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 13:52:40 +00:00
e8af776b99
Fixes for example bam files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4432 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-05 18:43:02 +00:00
efa60e5de5
and add changes to the vcf used in testing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3636 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-25 02:56:02 +00:00
18f62a346d
fixing the tests; Bamboo captured the failure in the logs correctly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3610 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 18:38:03 +00:00
55abfcc52f
adding file my VCF4 tests depend on
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3606 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 13:39:20 +00:00
cc3c18d3e1
a small dbsnp file for Tribble testing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2853 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-18 18:12:55 +00:00
66fc8ea444
GSA-182: Adding support for BED interval files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1767 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 02:45:31 +00:00
6e13a36059
Framework for ROD walkers -- totally experiment and not working right now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1600 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-12 19:13:15 +00:00
bdd0a6f9fa
change to make build work
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1511 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 13:43:10 +00:00
bb1d31914c
2009_02 release is no longer with us. Update the bam list.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1406 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-11 12:49:23 +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
08c4fb86e3
Derive examples from real data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1213 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-10 04:21:37 +00:00
9d659199f3
bam and fasta files generated with the artificial tools. These will be included in the GATK distro.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1151 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 22:49:31 +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
7834b969b4
Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@719 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 23:20:11 +00:00
8e9e2f4502
Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@716 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 21:06:28 +00:00
30218ee31a
Better validation scripts and data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@562 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 17:40:07 +00:00
40a2b3eeb3
Basic logistic regression support for calibrating qualities; mostly for Andrew to experiment with
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@529 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 19:09:50 +00:00
e842b543c9
Better validation scripts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@458 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 23:18:00 +00:00
f47f640df6
Better debugging output and testing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@455 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 21:54:56 +00:00
6c9d110eb9
better description
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@440 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 22:06:36 +00:00
2eabcfedb7
Fixed potential bug with next() operation returning empty contexts when a read contains a large deletion. We can now use the look ahead safely...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@439 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 21:41:30 +00:00
25ddc0f5ea
Skeleton of new directory structure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@34 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-11 20:05:05 +00:00
depristo
aaron
hanna
ebanks