8d294dd6e6
For the snps to create combine snps and filtered indels, now using a VCF with just snps instead of vcf with snps plus unfiltered indels.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5904 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-29 04:17:18 +00:00
b4d379584c
Commented out the generation of the GATKReport that I was using for debugging.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5903 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 22:15:09 +00:00
2a9c75c5ba
Throw an exception if the programmer tries to access a column that doesn't exist.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5902 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 22:08:48 +00:00
f3b38c0d3e
Fixed a bug in my math where I assumed the genotype likelihoods were normalized to 1.0 when they in fact are not. *Now* genotypes get altered when a different genotype configuration leads to a more consistent answer with regards to inheritance constraints. There's the question of what to do when two configurations are almost equally likely - I should probably filter those events out. But currently there is no threshold on the transmission probability.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5901 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 22:08:05 +00:00
5974675b43
Two intermediate commits, to work over the weekend.
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ReplicationValidationWalker: Just the skeleton of what will be the implementation of the replication/validation model.
dataProcessingV2: Committing an UNTESTED implementation of BWA alignment. I am running tests on it over the weekend.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5900 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 22:03:08 +00:00
69d9b5989f
documenting this walker as it may be useful to others in the future.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5899 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 21:58:51 +00:00
2524216d4b
Added the R script for VQSR
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5898 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 21:56:56 +00:00
77cae39c8e
Step towards tribble precompiled jar, support in build.xml for source with fallback to the checked in jar.
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Current tribble-129M.jar in SVN does not work with current version of GATK code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5897 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 21:04:27 +00:00
a50c40ed05
Temporary commit to aid in investigation of recent intermittent
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IndelRealignerIntegrationTest failures -- yes, it's the classic printf()
debugging technique. Will revert in a day or two once I get the data I need :)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5896 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 20:01:57 +00:00
260301016a
cleaned up the scripts and created an interval library to facilitate future reuse.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5895 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 19:35:36 +00:00
0048f1f6d3
Lots of interval_list file utility scripts
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1. findGenes : Parses the Genetic Association Database (from NIH) into an annotated 'genes of interest' interval_list file.
2. sortGenesByCoverage : combines the interval_list of the genes of interest with the report from GATK's DepthOfCoverage, generating an annotated interval_list with total and average coverages on each gene.
3. hasTheseTargets : Give it a list of targets (example: exon targets) and any interval_list (example: genes of interest) and it will generate an annotated interval_list of all the exons that are contained in the list of genes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5894 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 18:31:07 +00:00
2227f49220
misc cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5893 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 16:49:20 +00:00
9e834391fe
We now skip over all covering RODs in the BQSR as intended instead of just those which can be converted into a VariantContext. All the integration tests change because of subtleties in how certain dbsnp rod records are being converted into VCs. Added integration test which uses a bed file as the list of known polymorphic sites.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5892 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 16:32:17 +00:00
8ed82e5a08
The previous version of the UG was always creating BAQ'd pileups for the underlying site QUAL calculation. This resulted in some slowdown in the code. But as far as I can tell, the code actually didn't apply the BAQ'd base quality anywhere when the BAQ field wasn't in the read, so this just saves us 20% of the runtime when BAQ isn't enabled from heading into the BAQ subsystem when we don't actually want to get the BAQ'd base qualities.
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Fixed minor problem with WalkerTest for "" (for parameterization) md5s.
Added an explicit integrationtest for BAQ NONE
Now only creates the BAQ'd pileup, if the useBAQPileup parameter is provide in initializeAlternateAllele.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5891 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 14:00:52 +00:00
136c8c7900
ClipReads now supports HARDCLIP_BASES, though in fact this turned out to be not necessary for my desired tests. In the process of developing the HARDCLIP mode, I added some proper ReadUtils unit tests, which would ideally be expanded to include other ReadUtil functions, as added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5890 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 11:42:22 +00:00
549172af10
removing dependance on jobQueue == gsa
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5889 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 10:12:09 +00:00
a77ca2d36a
Incorporating Guillermo's patch to eliminate compile-time dependency of (core) UG indel model
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on oneoffs. Thanks Guillermo! We'll polish the patch when you free up a bit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5888 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 02:22:19 +00:00
fd21c5d100
Minor update so the debug messages don't show temp files as chromosome 208799060637697164972
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5887 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 22:56:33 +00:00
b4af28c7df
Handle case where -L argument (intervals) not given
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5886 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 20:24:56 +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
6ecbfa9013
OK, this time REALLY fix cut and paste error
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5880 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 19:47:12 +00:00
dab269160b
Added cofoja to the Queue package. Although BCEL doesn't think they're needed the scala compiler respectfully disagrees.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5879 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 17:42:34 +00:00
efe6602827
Fix copy-paste error from previous commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5878 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 16:02:08 +00:00
7a43673599
Bug fix: also enclose fetching FS or HRun in a try/catch block or else code will blow up if an annotation is absent (e.g. when there no evidence for a variant in a vc)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5877 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 15:00:36 +00:00
f7298f4a7f
First of many baby steps to redo way in which we trigger events for indel calling and to eliminate extended events: get rid of SpanningDeletions annotation for indels. It's completely useless, and even more so once we no longer trigger at extended events (because we'll trigger by definition a base before a deletion starts, so deletions present in the current pileup are not informative).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5876 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 00:49:23 +00:00
d393f59ad2
Moving the hg19 reference to a new location as per instruction from our intrepid leader
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5875 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-25 17:48:59 +00:00
bafdd4f8f7
Ask for existance of extended pileup before grabbing it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5874 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-25 17:39:03 +00:00
9d8c963fcc
Switched arguments from short name to long name.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5873 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-25 17:24:56 +00:00
6ec3dd0f8c
Updated GridEngineJobRunner to return status RUNNING instead of PENDING when a job has been sent to GridEngine, even if it hasn't started.
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Added GridEngine to pipeline tests.
Removed passing -jobProject since GridEngine projects must be predefined.
Writing the HybridSelectionPipelineTest yaml into the temp directory.
Disabled job priority as it needs to be refactored for use by GridEngine and LSF.
Fixed WholeGenomePipeline variantmergeoption rename to filteredRecordsMergeType.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5872 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-25 17:16:44 +00:00
3565eca2dd
Script to run UG to create annotated all-pop VCF files to use for Phase1 VQSR indel project consensus. Paralleles and generalizes SNP version, so in theory this script can be used for both SNP and Indel consensus.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5871 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-25 16:50:59 +00:00
3d134a8497
Updated to produce (actual) hg19 resources too
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5870 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-25 02:14:55 +00:00
389c546757
Renamed for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5869 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-25 02:12:21 +00:00
6ed71cf683
Annotation that adds a list of samples who are polymorphic at a site based on the GTs. Very useful if you are looking at rare variants among many samples, esp. in Evoker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5868 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 20:12:27 +00:00
1bd1404aa9
Sometimes md5s can be null
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5867 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 19:17:18 +00:00
e6396062c0
Script to use VQSR on indels - does VR, AR on each continental group, combines variants and then does VariantEval comparing with different chr20 all-pop 1000G callsets.
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Not for general use yet!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5866 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 17:19:30 +00:00
e582a92af6
WalkerTest now checks for valid md5s in the integrationtests themselves, so no more stray whitespace errors. Added a WalkerTestTest to ensure tha t bad MD5s are detected and an error thrown
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5865 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 14:34:55 +00:00
0448ef28d3
Actually use the right parameter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5864 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 12:09:01 +00:00
06486c134a
Kill extra space in the md5.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5863 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 12:00:31 +00:00
d551ce720d
Updated with new CombineVariants syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5862 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 11:38:09 +00:00
57e4693e4c
Slightly better error message when failing to create the index on the fly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5861 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 11:04:08 +00:00
cf3dbfee97
Renamed variantMergeOptions to filteredRecordsMergeType, as this is really what it does. Cleaned up the wiki so that it's clear what this does, as well as included an example of how to create an intersection with CombineVariants and SelectVariants. Added integrationtests of CombineVariants with OMNI and HapMap that deal with the two ways to merge fitlered/unfiltered records at the same site.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5860 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 01:54:29 +00:00
653475ce12
Now finds the most likely configuration of genotypes given the genotype likelihoods and inheritance constraints. The parental genotypes are now phased as well (the alleles are ordered as A_transmitted|A_untransmitted). Rewrote the way the transmission probability is calculated. This will probably move into core soon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5859 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 01:35:40 +00:00
2efd807952
No more default callsets, they're now mandatory arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5858 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 21:56:43 +00:00
133712faec
Have a list of bam files but Picard updated their versions from v1 to v17 ? This script will update all your v* numbers for you.
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PS: don't hate Lua. :-)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5857 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 21:46:14 +00:00
4bfec4c55b
Reenabling E.coli ValidatingPileup with MV1994 realigned using the BWA/C bindings.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5856 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 21:32:53 +00:00
bc4305c956
Added memory limit parameter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5855 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 21:11:44 +00:00
kshakir
kiran
carneiro
droazen
rpoplin
depristo
hanna
fromer
corin
delangel
ebanks