7185fcb47b
Committing my notes about the methods development pipeline so we stay synced up while I'm on vacation. Cheers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4891 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-21 21:14:20 +00:00
80770dc032
Expanded target pipeline complete. Stop trying to be clever about scatter-gather; wait until functional SG is built-in to Q. Til then, a lazy version of the fullCallingPipeline. Seems to take a long time to generate the graph though...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4888 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-21 00:56:16 +00:00
758d14a261
Checking in scripts used for testing the linear index MAX_FEATURES_PER_BIN.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4887 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 21:25:36 +00:00
fc33901810
Graph structure must be known at compile time. Removing GroupIntervals until a future point where in-process-functions can predict their output based on inputs [though this is probably forever: the inputs may not exist at compile time!]
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4886 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 21:22:58 +00:00
61d5daa65c
EXTREME interval processing. Still undergoing testing.
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+ GroupIntervals allows user-defined scattering (e.g. take an interval list file, split it into k smaller interval list files by number of lines)
+ ExpandIntervals expands the intervals, either by widening them, or allowing the definition for nearby intervals (e.g. flanks starting 1bp before and after, ending 10bp after that)
+ IntersectIntervals takes n interval lists, writes 1 interval list that is the n-way intersection of all of them
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4885 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 19:42:50 +00:00
4ca1da1d07
Updating the NA12878.HiSeq bam file to be the correct bam file in the methods development qscript.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4879 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 14:53:10 +00:00
8fac346ac1
Misc cleanup in Methods Development Qscript
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4878 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 04:24:25 +00:00
34ab5b4889
Turning on BAQ in Methods Development pipeline. A new dataset is added: 363 EUR samples from the November 1000G release.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4877 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-19 21:13:25 +00:00
8118a439c0
Commit for Khalid
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4876 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-18 22:24:18 +00:00
15a33545f4
Updating Methods development pipeline qscript with the bam lists for all the data sets. It is ready for people to start running with it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4875 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-18 22:19:14 +00:00
f0ab7b849a
Adding a window size variable to avoid indel genotyper error
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4873 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-18 04:19:54 +00:00
bdef4e775a
Initial checkin of methods development pipeline qscript. It allows the methods dev team to run an overnight job which calls and recalibrates a variety of data sets and allows for an end-to-end sanity check of final results for potential changes to the methods. It isn't meant to be used by anybody quite yet, but shows the general structure and flow.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4871 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 22:14:02 +00:00
095fc1922a
By popular demand I'm adding the qscript I used to do the 660 bamfile 1000G calling for ASHG. It does cleaning, BAQing, and merging in 3mb chunks genome-wide then calls SNPs on those temporary bams.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4866 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 18:49:03 +00:00
32d5397c01
Experimental support for sided annotations. Currently not more/less valuable than two-tailed testing. Future experiments are needed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4864 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 15:08:31 +00:00
0d18bd1011
Now that addAll() is in the superclass, no longer need this definition (which, without override, prevents the script from compiling anyway)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4862 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 05:36:31 +00:00
3e75431bc8
Thanks to mark: VCFInfoToTable removed in favor of a more flexible walker. Slight change to the argument structure of the walker to make it play more nicely with Queue: the field list parsing is pushed into the command line system (e.g. the variable is exposed as a List<String> and not a String, so Queue doesn't have to join a list into a string only to have it broken out again. This also allows the user to specify -F field1 -F field2 -F field3 if he/she so desires.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4842 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 03:33:36 +00:00
2217837845
Commit for Khalid -- should be a scala version of vcf2table but for some reason the run method isn't getting called.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4841 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 00:44:15 +00:00
f36861eeee
One more little bfix -- the issue was not the grep command, but instead the NFS in the awk; i changed it to ++count in the last commit which was really responsible for the fix. Then this ultra-escaping semi-broke teh grep again.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4831 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 20:36:14 +00:00
d34c5640d2
Bugfix for clf version of extract samples. Due to dynamic shell creation and bsubs and whatnot, the OR pipe for grep ("a|b") needs to be super-escaped ("a\\\\\\\\|b").
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4829 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 19:06:30 +00:00
f795b25c47
In-process versions of sample extraction and interval-list conversion for VCF files. Required an in-process-function branch of the queue library.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4827 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 17:36:53 +00:00
e219f6a4b5
Q script to run VQSR on a whole variety of common data sets. To be used as a basis for general methods development pipeline
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4826 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 16:55:52 +00:00
7bc2049031
Updates and bug fixes to private mutations qscript and pipeline libraries. Hand filter strings are now not busted (boo to having to escape quotes); convenience method added to VariantCalling to propagate standard trait data to a given GATK command line -- should be made more scala-esque in the future.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4824 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 04:55:13 +00:00
cf75caf653
java changes:
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VariantEvalWalker's logger is made public, so that variant eval modules can access it through the parent object.
DesignFileGenerator comment lists how best to bind things to it, and the feature accessor is better refined to grab the genome loc. (old change)
scala changes:
convenience addAll( List[CommandLineFunction] ) added to QScript class (and thus removed from the fCPV2)
useful command line functions added to a new library package for command line functions (these are fast simple VCF command lines)
bug fixed in ProjectManagement for the class where there's only one batch to be batch-merged (not really part of the use-case, but an edge-condition that came up during pipeline testing)
first draft of a private mutations pipeline which will be elaborated in future
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4823 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-12 05:10:45 +00:00
81290d238d
Restructuring my qscripts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4821 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-11 20:58:45 +00:00
56433ebf6b
Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects:
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- bsub command line is no longer fully printed out.
- extraBsubArgs hack is now a callback function updateJobRun.
Updated FullCallingPipelineTest to reflect latest changes to fullCallingPipeline.q.
Added a pipeline that tests the UGv2 runtimes at different bam counts and memory limits.
Updated VE packages that live in oneoffs to compile to oneoffs.
Added a hack to replace the deprecated symbol environ in Mac OS X 10.5+ which is needed by LSF7 on Mac.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4816 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-10 04:36:06 +00:00
27acede64d
Removing old arguments. We'll now be running with the defaults.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4811 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-09 18:58:56 +00:00
f8dd59c1d1
Tightening of the batch merging pipeline. Optimized to run on hour queue, so please: if you run this, crush 'hour' with it. Testing is forthcoming, but it merged 700 samples overnight.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4805 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-08 14:36:23 +00:00
f4c43f013f
Due to the overhead for reading VCF files (>32g for 700 5MB VCF files), batched merging has to generate likelihoods in batches.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4796 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-06 18:23:54 +00:00
0944184832
Major refactoring of library and full calling pipeline (v2) structure.
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Arguments to the full calling qscript (and indeed, any qscript that wants them) are now specified via the PipelineArgumentCollection
Libraries require a Pipeline object for instantiation -- eliminating their previous dependence on yaml files
Functions added to PipelineUtils to build out the proper Pipeline object from the PipelineArgumentCollection, which now contains
additional arguments to specify pipeline properties (name, ref, bams, dbsnp, interval list); which are mutually exclusive with
the yaml file.
Pipeline length reduced to a mere 62 lines.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4790 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-05 02:33:54 +00:00
bdc7516168
Taking out recalibrating for now, since having these files is confusing people and we've not gone to dbsnp 132 yet so cluster generation's broken with these command lines.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4786 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 22:12:09 +00:00
220fb0c44a
Added a pipeline for merging batches. For now takes a file containing a list of VCFs, and a file containing a list of bams. Does not do anything smart (e.g. if you leave out some .bams or add some extra ones, you will not be warned). Heavy lifting done in (the beginnings of) a library for managing multi-batch or multi-project tasks.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4771 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 07:31:59 +00:00
9f03f09cc9
Changes to V2 pipeline and libraries. AB dropped. Cleaning enabled. Project name now properly propagated to intermediate files (instead of the string repr of the object). Indel mask is now expanded prior to filtering at indels.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4769 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 18:55:48 +00:00
06a0fb4489
Library-ized pipeline now functions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4759 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 21:34:59 +00:00
4413208c45
Removing unnecessary and incorrect includes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4752 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 02:06:48 +00:00
6b70cde0b9
Adding a forgotten quote mark
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4729 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 16:38:27 +00:00
e15d18129c
Adding by sample metrics. Not sure why we didn't have this in here in the first place
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4723 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-23 21:36:03 +00:00
fe28f8da9c
Removing Uniquify from main pipeline indel merge, since the pipeline isn't merging from samples with the same name anyway.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4721 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-23 17:25:22 +00:00
28805d17ca
Commenting out allele-balance for now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4715 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-22 16:48:08 +00:00
8dca5bd861
Putting the annotation back in, both to the filters and to UG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4709 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 21:02:15 +00:00
da1fe5bb37
Removing the AB filter given that we don't have that in the VCF anymore
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4708 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 20:22:05 +00:00
302cc13735
Trying out Queue for the first time.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4705 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 18:29:12 +00:00
5466365575
Fixing a silly typo
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4680 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 18:16:51 +00:00
a64f693b20
Updated pipeline script to include dbSnp for UG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4679 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 18:09:47 +00:00
801c562909
Now actually checking in the integration test mentioned in the prior commit: compiles the full calling pipeline.
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Removed QScript usages of VariantRecalibrator's -reportDatFile, --report_dat_file
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4668 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-14 04:27:10 +00:00
673fa841a4
Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.
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Removed obsolete usages of PackageUtils with updated PluginManager.
Ported Queue interval utilities written in scala over to Sting's java IntervalUtils.
Added a very basic intergration test to ensure that the fullCallingPipeline.q compiles.
Added options to specify the temporary directories without having to use -Djava.io.tmpdir (useful during the above integration test).
While adding tempDir added options to specify the run directory from the command line, for example "-runDir v1".
Upgraded to scala 2.8.1 and updated calls to deprecated functions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4661 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 20:14:28 +00:00
c19f567424
Sometimes, inputs are really outputs in disguise.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4631 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-05 19:51:16 +00:00
0e40321a52
Brütall hack: make the bam list creator job wait for the interval creator job, so that there is an implicit dependency of UG on the interval list, by way of the bam list
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4628 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-04 20:43:11 +00:00
cb0b2f9811
My analysis script for private mutations. I'm committing it because it contains a number of specialized command line functions that could prove useful in the future. (For example: ConcatVCF and ExtractSample)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4626 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-04 19:57:27 +00:00
42e9987e69
Bug fix to GenotypeConcordance. AC metrics get instantiated based on number of eval samples; if Comp has more samples, we can see AC indeces outside the bounds of the array.
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Bug fix to LiftoverVariants - no barfing at reference sites.
AlleleFrequencyComparison - local changes added to make sure parsing works properly
Added HammingDistance annotation. Mostly useless. But only mostly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4622 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-03 19:23:03 +00:00
5cdd7a7ba4
There's no such thing as a sam index, so the GATK extension generator doesn't need to add an @Input for them.
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Updated a call to swapExt to specify the directory.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4586 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-27 20:39:03 +00:00
rpoplin
chartl
kshakir
corin
depristo
ebanks
kiran
hanna