eb67aee732
bug fix: forgot to uncomment code to compute genotype likelihoods
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4397 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-30 21:38:22 +00:00
ece694d0af
Next iteration on new UG framework:
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- Brought over exact AF estimation from branch (which is now dead). Exact model is default in UnifiedGenotyperV2.
- Implemented completely new genotyping algorithm given best AF estimate using dynamic programming, which in theory should be better than both greedy search and any HWE-based genotyper.
- Integrated and added new Dindel likelihood estimation model.
- Corrected annotators that would call readBasePileup: since we can be annotating extended events, best way is to interrogate context for kind of pileup and either readBasePileup or readExtendedEventPileup.
All changes above except last one are still in playground since they require more testing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4396 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-30 21:33:59 +00:00
027241e1ca
Moved the test classes from java/classes/testclasses to java/testclasses. Update your IntelliJ settings!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4395 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-30 20:42:41 +00:00
4ea73bcfb1
Basic unit tests for WalkerManager.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4394 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-30 19:27:41 +00:00
bf7fd08810
Fix newly-introduced bug in the PluginManager/DynamicClassResolutionException
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where, when the system can't find a plugin of the correct name, the system
prefers to crap all over itself and throw an unintelligible NullPointerException
rather than displaying an intelligent error.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4393 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-30 19:07:05 +00:00
14e19f4605
(Slightly) better exception text when SAM/BAM output file can't be created.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4392 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-30 18:43:22 +00:00
1fb8c86f6d
Looks like we've got two competing models for an empty interval list: null and
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the empty list. Score another victory for the integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4391 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-30 17:11:47 +00:00
78343be52c
At some time in the recent past, we lost our ability to process the '-L all'
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argument. Brought it back, and added an integrationtest to make sure it
stays around.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4390 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-30 15:58:43 +00:00
f34b4c6b82
Be smarter if the beagle output is set such that getParent() returns null. Up the memory limit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4389 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-30 12:48:47 +00:00
0142047da9
And a bugfix 3 seconds later. Don't tell java to use up to 20g while telling the farm to kill the job if it tries to exceed 4g.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4388 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-30 02:08:47 +00:00
06970ae039
A qscript that refines genotypes with beagle and merges them into one vcf (running currently on the recent chr20 production calls).
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This will be librarized soon; but if you need to do something like this, feel free to cannibalize.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4387 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-30 02:05:30 +00:00
e80742e72f
Use -o as argument for output file in ProduceBeagleInputWalker, to be consistent with other walkers (you're welcome, chartl :)).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4386 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 22:46:39 +00:00
732aa32758
Every Sting app from now on will be forced into the US English locale.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4385 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 21:55:21 +00:00
20ffe484bc
Added detection and INFO field marking of phasing inconsistencies (and optional filtration using --filterInconsistentSites)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4384 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 19:28:56 +00:00
a6c7de95c8
By using the AC info field instead of parsing the genotypes we cut 78% off the runtime of VariantRecalibrator. There is a new argument to force the parsing of genotypes if necessary. Various other optimizations throughout.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4383 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 18:56:50 +00:00
2d1265771f
Fix for G: make sure to generate the genotype conformations in the grid for the target frequency when not using grid search for anything except the conformations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4382 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 16:44:53 +00:00
4556e3b273
First iteration in filling up exact AF calculation with new refactored UG. Code computes EM iterations of exact AF spectrum and returns to caller.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4381 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 16:21:54 +00:00
2708e83198
For show (Queue works nicely): An analysis script that runs QC for the omni chip
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4380 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 15:04:17 +00:00
0d71dff928
Small bug fix to the new UG (need to initialize the entire posteriors array) means that we also get identical results as old UG when calling with 60 samples in the pilot1 data. Now that I'm happier with UGv2, I've transitioned it to use the correct AF priors instead of the busted ones still in the old UG.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4379 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 14:24:50 +00:00
eee134baf2
Chris found a bug in the downsampler where, if the number of reads entering
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the pileup at the next alignment start is large, we don't add as many of those
incoming reads as we should. No integration tests were affected.
Thanks, Chris!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4378 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 11:18:12 +00:00
0ec07ad99a
Initial version of refactored Unified Genotyper. Using SNP genotype likelihoods and GRID_SEARCH AF estimation models, achieves the exact same results as original UG on 1-2 samples with the exception of strand bias (not implemented yet); other than that I have no idea. Needs tons more testing. Do not use. For Guillermo only.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4377 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 08:42:25 +00:00
6df7f9318f
For enums generate the full path to the Enum type to avoid collisions such as enum Model and enum Model used in the same class.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4376 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 05:28:59 +00:00
cfebe5c731
clean-up the docs a little
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4375 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 05:02:41 +00:00
702449d835
adding a Python script to roll back tribble to the correct version, for users who want to checkout historical versions of the GATK code. This code cross references the current checkout date with the Tribble logs, and pulls the closest (price-is-right style) revision.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4374 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 05:01:46 +00:00
e322e71c2f
Restored SVN history for phasing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4373 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 00:02:02 +00:00
720aaca8a0
Trying to restore SVN history for phasing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4372 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 23:50:28 +00:00
bf88117ead
Trying to restore SVN history for phasing directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4371 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 23:48:24 +00:00
dfb5143a41
Restore folder
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4370 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 23:46:07 +00:00
7c909bef82
Moved phasing classes out of playground! The code is still under production, though...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4369 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 23:21:28 +00:00
8d8980e8eb
Fixed phasing algorithm to: 1. More correctly weed out irrelevant reads and sites; 2. Crudely flag sites with large phase discrepancies betweens reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4368 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 23:02:53 +00:00
5a5c72c80d
Accidentally commited some debug output to PackageUtils, reverting change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4367 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 21:58:42 +00:00
a90fb64c03
Added 'Cron' to subject for easier message filtering
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4366 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 21:03:50 +00:00
862c94c8ce
Small change for Matt -- output partition types in lexicographic order.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4365 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 20:08:03 +00:00
7ad87d328d
Make sure to uppercase ref bases since they aren't coming from the engine
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4364 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 19:05:46 +00:00
37613810bf
Tired of writing vcf_hg18_to_b36 over and over again when necessary. Added a -r flag to this script that does it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4363 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 14:51:57 +00:00
96cccafb0d
Adding a few helper methods for accessing sample metadata, and associated unit tests. These are motivated by discussion with Ryan about how he'll use sample metadata in VariantEvalwalker - hopefully will make it easier for him. Methods are:
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-- getToolkit().subContextFromSampleProperty(): filters a VariantContext to genotypes that come from samples that have a given property value
-- getToolkit().getSamplesWithProperty(): gets all samples with a given property
-- getToolkit().getSamplesFromVariantContext(): sample objects that are referenced by name in a VariantContext
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4361 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 02:16:25 +00:00
51fdf9d701
Default memory limit is now 4g (apparently necessary when testing on full 100-sample Autism_Daly dataset)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4359 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-27 05:43:08 +00:00
a7815b4268
Nightly test for Queue-based pipeline.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4358 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-27 05:24:58 +00:00
1034853a84
Adding 'solexa' to list of known/supported platforms
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4357 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-27 02:38:38 +00:00
bcc09f5d8c
Simplifications: removed command-line arguments to control SNP cluster filter parameters. Infer the number of contigs to scatter indel cleaning from the contig list (which we should get rid of too). Changed the PY argument to just Y for specifying the path to the YAML file. Cleaned up command-line argument documentation. See http://iwww.broadinstitute.org/gsa/wiki/index.php/Queue-based_pipeline for a list of remaining issues.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4356 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-26 22:50:30 +00:00
9820a12fa5
Removed unnecessary dbSNP big-table dependency. Ti/Tv is now required. Consistent downsampling level for all programs. Spelling corrections. VariantEval now generates R-style output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4355 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-26 16:55:58 +00:00
145fb0df8b
Changed the wait job's dispatch queue from short (which doesn't exist anymore) to hour
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4354 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-25 23:36:49 +00:00
9bfbc3b784
Commented out changes to ADPR and VariantEval modules that are causing this script to not compile.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4353 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-25 15:12:10 +00:00
70f03a7113
first pass of well-formatted tribble exceptions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4352 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-25 03:29:33 +00:00
edaa278edd
Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance.
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This will allow other programs like Queue to reuse the functionality.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4351 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-25 02:49:30 +00:00
497bcbcbb7
Recent changes to the build system make the build system complain loudly about
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pieces of core that depend on playground. Most of these have been eliminated by
(temporarily) promoting Aaron's report system to core in this checkin. I'll
follow up with other changes in separately.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4350 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 22:09:12 +00:00
6ebca5d219
Enhancements to build external projects for walker sharing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4348 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 21:17:16 +00:00
eb1fa4bff3
changes an argument to an output so I can use it to track dependencies in queue
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4347 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 21:07:09 +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
3ec0e09edd
ADPR is now included in the full calling pipeline. The most up to date version of the ADPR is about to be committed and should be used with the script for now. The qscript now calls for two additional strings as inputs: the sequencing machines used and the sequencing protocol. In order for ADPR to finish successfully, a squid file for both the lane and sample level data needs to be produced, reformatted and named <projectBase>_lanes.txt or <projectBase>_samps.txt, respectively. These files need to be in the working directory. When database access is ready, this and the protocol and sequencer parameters of the r script will go away.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4345 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 19:28:43 +00:00
delangel
kshakir
hanna
chartl
fromer
rpoplin
ebanks
aaron
kiran
bthomas
corin