2a80ffa2ee
Totally experimental, barely useable not to be used yet implementation of an "Indel Quality Recalibrator" Idea is that any indel that's not in input dbsnp is treated as an artifact, and then a csv is built with # of indels and # of observations as a function of each input covariate (initially, only cycle, read group and homopolymer run are useful). Then, when computing likelihoods of indels based on input haplotypes we compute gap penalties based on value of covariates at read. Feature is disabled by default with hidden arguments. TBD if usefulness of feature is worth the extra time and pain.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5724 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 20:31:43 +00:00
3224bbe750
New visualization output for VQSR. It creates the R script file on the fly and then runs Rscript on it. Adding 1000G Project consensus code. First pass of having VQSR work with missing data by marginalizing over the missing dimension for that data point (thanks Chris and Bob for ideas). Updated math functions to use apache math commons instead of approximations from wikipedia. New parameters available for the priors based on further reading in Bishop and looking at the new visualizations. Updated integration test to use more modern files. Updated MDCP to use new best practices w.r.t. annotations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5723 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 19:14:42 +00:00
fcf8cff64a
We didn't actually support all of these extensions. Updated to be accurate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5722 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 19:03:46 +00:00
a93a9ac663
adding gold standard (full coverage) to the variant eval analysis output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5721 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 16:29:11 +00:00
f76e2791a9
Update to work with latest eval format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5720 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 13:44:50 +00:00
139ae79d9e
Update to work with latest eval format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5719 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 13:21:23 +00:00
2d81262f87
Fixed a bug where empty intervals were being scattered zero ways parallel. Would be awesome to use the GAE at some point.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5718 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 22:42:48 +00:00
2384e23274
Added the capability of running count covariates only on a given interval.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5717 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 21:30:14 +00:00
34092fd32f
minor update...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5716 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 21:29:01 +00:00
36ac8beee1
Making the GATK unpredictably random...
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through an option!
set -ndrs if you want the GATK to be really random (non-deterministic). Engine option, available to every walker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5715 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 19:29:08 +00:00
f97e7d2fb4
Walker that calculates the percentage of bases that are covered to at least 20x. Very useful! In oneoffs until someone else thinks it's as useful as I think it is ;)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5714 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 19:19:39 +00:00
3868a7e778
Oneoff project to downsample, bootstrap and call snps to test sensitivity/specificity of downsampled coverage in WEX projects.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5713 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 19:17:30 +00:00
deed7c47a1
Continuing the epic fail, some of our existing integration tests were wrong because of the lazy loading failure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5712 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 17:54:41 +00:00
ab9ffb1a74
Epic failure on the lazy loading of genotypes: if the input VCF had its samples unsorted and we used a walker that didn't require genotypes, then we would sort the samples but not load genotypes (and therefore the genotypes wouldn't match the samples anymore). Added simple integration test to cover this case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5711 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 16:03:45 +00:00
96571b55be
Disable caching of ReadShards by the GenomeLocProcessingTracker (at least
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temporarily). Unfortunately this does not completely fix the IndelRealigner
exception that Ryan is seeing, but it helps things quite a bit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5710 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 13:59:34 +00:00
a5b96e0e04
I have to remember that this is Java, not C.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5709 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-28 17:40:14 +00:00
f04cc4321f
fixed a bug when the pipeline was used on a single bam.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5708 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-28 17:19:22 +00:00
b7334dcc1e
Rank sum test annotations are the Z-scores from the test instead of the p-value.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5707 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-28 14:35:00 +00:00
45081c32d7
continuing from last night, the integration tests weren't covering the right behavior either
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5706 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-28 13:30:57 +00:00
f34e6d5b8c
Somewhere along the way someone broke this tool and failed to update the documentation to boot. Fixing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5705 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-28 03:16:20 +00:00
ae8f3f2cde
Check for bad reference bases before creating simple/'empty' VCs. Updated the code in the indel GL model to be consistent and to use the existing utility in the Allele class.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5704 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 23:55:20 +00:00
122d5845d3
GATK Resource bundle, latest version (now with b37 -> b36 support). Oneoff scala script that assesses chip coverage of calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5703 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 22:01:36 +00:00
6cce3e00f3
A test walker that does consensus compression of deep read data sets.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5702 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 22:00:48 +00:00
3907377f37
When genotyping given alleles, for multiallelic sites we go back to the reads and use the alternate base with the highest sum of quality scores instead of taking the first alternate allele from the vcf file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5701 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 21:31:09 +00:00
6e9e766a71
The tighter interval validation wasn't interacting well with unmapped
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intervals -- altered the validation methods to not throw an error for
unmapped intervals.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5700 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 20:56:46 +00:00
6d5e45b5c6
Revbump Picard dependencies at Tim/Kathleen's request. Exclude anonymous
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classes from PluginManager.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5699 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 20:38:05 +00:00
d650efd40a
Fix for bug GSA-449: Intervals that are not in GATK format are not validated
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to the same standard as GATK format intervals. Full validation against contig
bounds is now performed for all intervals, regardless of their source. Also
fixed a few tests for validation exclusions that were backwards.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5698 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 18:12:10 +00:00
df35a143b2
Removed -debug/--debug_mode.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5697 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 10:56:39 +00:00
ca817356b6
Quick disabling test to restore build. TODO fix test or complete removal of the MFCP.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5696 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 04:26:11 +00:00
27495a0c64
Killed quiet mode. Should probably kill debugMode as well, but Queue's using
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it. Will check with Khalid tomorrow.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5695 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 04:17:36 +00:00
6b1b4931e7
Added FCP VE stratifications for Filter, FunctionalClass, and Stratification as requested by Corin.
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Feeding FCP UG the bam list instead of individual bams to cut scatter gather time from O(m^100) as measured by Chris to O(m^1).
Fixed NPE when eval values aren't found in PipelineTests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5694 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 02:29:56 +00:00
f3dacd3c40
Use ByteBuffer.allocateDirect() instead of ByteBuffer.allocate().
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ByteBuffer.allocateDirect() behaves like Java NIO MappedByteBuffers in that
it consumes address space, which counts against our virtual memory allocation;
but cannot be destroyed or otherwise freed. This was definitely contributing
to the LSF failures that I was seeing, but I'm not yet convinced that it's the
sole source of these virtual memory 'leaks'. More tomorrow as the results of
my whole exome tests start to roll in.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5693 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-27 02:01:11 +00:00
7afeb1ab17
Removing broken imports (boo)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5692 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-26 18:55:25 +00:00
379f837e82
RankSum z-scores are looking quite good, so RIP Wilcoxon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5691 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-26 18:34:39 +00:00
bc3fd70b0a
Removing the old association walker, switching test to just validate that MannWhitneyU is doing the right thing. Unit tests still pass.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5690 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-26 18:05:19 +00:00
b915520653
Updating to apache commons math v2.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5689 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-26 17:31:49 +00:00
58c7b27ccc
Missing file from last checkin.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5688 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-26 00:12:41 +00:00
f619dd3ca7
Refactored IntervalUtils used to parse and scatter intervals for Queue.
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Scattering non-contig interval lists by number of loci in the intervals instead of just number of intervals.
Queue caches the list of locs and how to split them up instead of reloading them from disk repeatedly.
TODO: general purpose function to divide data evenly.
Skip over comments when parsing picard analysis files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5687 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-26 00:06:00 +00:00
6ca4e3cebf
Updating FCPT nCalledLoci due to fixed QD<2.0 filter.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5686 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-25 21:37:04 +00:00
ed6da6f72d
Added JavaMail dependencies to Queue package since bcel wasn't picking them up.
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Added the ability to add a file path to a package.
Checking for missing files when packaging.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5685 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-23 20:48:40 +00:00
1158c99726
Only running chr20 test on the hour queue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5684 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-22 22:09:42 +00:00
57a4700299
Ported small BAM performance test suite to the Google Caliper microbenchmarking suite. Looks promising,
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but I'm still not sure that GC is a good long-term solution.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5683 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-22 22:09:17 +00:00
00b57c751b
Added missing ".0".
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5682 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-22 21:50:07 +00:00
a56a2dfdb7
Nothing to see here. Move along.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5681 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-22 15:01:02 +00:00
8bc93046f4
Adding chain files for Mark. Tested by lifting over back and forth between builds. Note that they comprise only the standard contigs so no _randoms or GL000xxx.1s.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5680 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-22 14:53:15 +00:00
600617a63c
Enabled code to deal with hard-clipping adaptor sequence when processing reads in pileup in indel caller. Proven now that changes are minimal (4 less calls in NA12878 chr20, quals slightly different), minor changes in vcf fields in integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5679 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-22 14:10:33 +00:00
e050d94df4
Renaming because they actually map to b37, not hg19
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5678 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-22 13:34:48 +00:00
831ad0cd1a
Quit immediately with an error message if any of the individual steps fails.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5677 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-22 13:23:33 +00:00
88735a8c9b
Adding in a delta to try and better measure effect size -- equivalent to looking at the lower end of the N^th percentile confidence interval. Kind of a hacky way to add it in, the infrastructure is about due for a streamlining rewrite.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5676 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-22 03:53:33 +00:00
7428ae338a
A fix for Marian Thieme's NPE in the new sharding system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5675 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-21 19:47:14 +00:00
delangel
rpoplin
ebanks
carneiro
corin
kshakir
hanna
depristo
droazen
chartl