4d08d39849
Moved some of the java to scala conversions from production to test code as it's not needed in production and slows down the code.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5769 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-05 04:11:15 +00:00
28b897d5de
Fixed O(N^2) operation when scattering interval files.
...
Cleaned up intervals contig count function.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5768 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-05 03:32:35 +00:00
3882d1b9c0
fixing the build \o/
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5767 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-05 00:57:49 +00:00
8ad547e6c2
Fixed another interval bug where dividing up N intervals into N parts wasn't working.
...
Minor updates to the FCPTest to match the changes due to using the old indel caller.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5766 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 20:49:35 +00:00
825682f58c
oops, putting the script back into a sensible state
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5765 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 20:17:05 +00:00
b5ab2274f6
Committing the base qscript I used to make the Phase1 Project Consensus. Does per-population cleaning and simplifyBAM, and then per-analysis-panel calling with genotype given alleles. Combines info fields using the panel with max AC.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5764 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 20:13:26 +00:00
b4654b0f47
Status messages to user added
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5763 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 20:10:47 +00:00
bcc688c1e9
small formatting change
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5762 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 20:01:20 +00:00
1410327901
Cmd line argument reference fix
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5761 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 20:00:14 +00:00
5c6965575e
Some refactoring that Mauricio and I worked through together. Changed filters
...
to extend from org.broadinstitute.sting.gatk.filters.ReadFilter rather than
directly from net.sf.picard.filter.SamRecordFilter, which allows us to add
an initialize(GATKEngine) method so that filters can do any initialization
they'd like based on CL arguments, SAM headers, etc.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5760 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 19:29:08 +00:00
b66c6dced1
- No longer prints out non confident calls (they were leading to tables that don't add up and confusing some Pacbio folk).
...
- Added sensitivity and Specificity to the report.
- With the changes in genotype likelihoods, the indel analysis only happens if the BAM file also has an extended event. Not great, but at least it's not broken.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5759 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 19:26:55 +00:00
4d251fb91f
Why won't you die?
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5758 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 19:13:39 +00:00
f7d9f0a1f3
Removing QPipeline directory as there's no one to support it at the moment.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5757 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 18:36:02 +00:00
7ed8b4ddb0
Making sure CalculateLikelihoodsAndGenotypes returns an empty variant context when 'EMIT_ALL_SITES' and 'GENOTYPE_GIVEN_ALLELES' are being used, now for indels too!
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5756 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 18:04:56 +00:00
3e8fc71743
Missing parenthesis for database access commands added
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5755 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 16:59:17 +00:00
23efd66d31
Updated Tearsheet with by sample QC metrics, bugfix for misnamed variables
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5754 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 16:57:48 +00:00
72a07e4553
Updated Tearsheet with by sample QC metrics, bugfix for misnamed variables
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5753 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 16:54:05 +00:00
2e1c09c03b
Updated tearsheet drop
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5752 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 16:47:47 +00:00
f386cad58c
Updated Tearsheet with by sample QC metrics
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5751 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 16:47:26 +00:00
6c7a0adc76
Updating VariantGaussianMixtureModelUnitTest to use truth sensitivity cutting
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5750 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 13:56:01 +00:00
08f0509a5c
Disabling the queue/pipeline package by default so that scala code can build. If it's not going to be fixed the package should be removed. If it is going to be fixed this patch to build.xml should be reverted.
...
Also added the old model of indel calling to the FCP.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5749 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 12:17:33 +00:00
a19389528d
Bring back from the dead the old likelihoods model for indels, which has worse performance but is about 4x faster. Enabled with argument -GSA_PRODUCTION_ONLY in UG
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5748 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 22:38:33 +00:00
f35d955490
recalibrates a dataset splitting between good and bad regions for comparison (used to be named justRecalibrate)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5747 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 21:43:09 +00:00
9f2a8033ff
just recalibrates now recalibrates one sample, fully, not splitting intervals (naming makes more sense)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5746 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 21:42:23 +00:00
c2f8536e02
removing old GATK options
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5745 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 21:40:39 +00:00
8bb92160b5
Script to identify mendelian violations in the CEU Trio and follow up with supposedly incorrect SNP calls
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5744 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 21:19:42 +00:00
e2b9227d8d
script to test BQSR on good/bad regions
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5743 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 21:16:37 +00:00
e5cc0f4eec
Added 'specificity' to variant eval's Validation Report evaluator.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5742 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 20:48:30 +00:00
b88dec387c
clean up from VQSR movement
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5741 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 20:35:30 +00:00
23cd3a7a5d
Moving VQSR v2 to core.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5740 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 20:20:06 +00:00
44a717f63a
Good bye VQSR v1. This commit will break the build.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5739 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 20:09:52 +00:00
2dacf1b2b2
Better header support when running R's read.table(...,header=T).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5738 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 19:56:20 +00:00
ad8c786b2d
Now more easily R-parseable.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5737 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 19:30:50 +00:00
5bade81c6d
Adding tranche plot generation back to VQSR
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5736 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 19:26:26 +00:00
e73720c2db
Updating VQSLOD annotation description
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5735 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 19:01:08 +00:00
11052918d9
Better exception text for common error in VQSR.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5734 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 18:37:25 +00:00
4bbce42861
Renaming ContrastiveRecalibrator --> VariantRecalibrator in preparation for move to core
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5733 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 18:12:47 +00:00
6323fb8673
misc cleanup in VQSR
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5732 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 18:00:22 +00:00
f3bd11a02e
Dress up some formatting issues.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5731 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 17:35:18 +00:00
9c809ed68e
A walker to analyze the memory consumption of reference, reads, and RODs at
...
each base both in bytes and as a percentage of the used heap size.
May be a bit buggy at this point; there are a lot of metrics around the Java
heap and I'm not completely sure that the metrics I'm outputting are exactly
the ones that I'm looking for.
Also fixed a documentation bug in my Sizeof class.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5730 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 17:08:15 +00:00
d4cbd8691c
Make the default that we only output SNPs (so that when I make another release we don't get flooded with questions about why the UG is all of a sudden so slow)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5729 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 16:38:55 +00:00
70f8ab6f89
Adding AF bin stratification for VariantEval.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5728 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 15:22:50 +00:00
870e65a685
Fixing a build failure because I want to be completely sure that the code I
...
checked in immediately following the build breaking code passes integration
tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5727 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 02:09:53 +00:00
411980a50a
Performance enhancements in GATKBAMIndex. Not sure these will assist in a
...
normal use case, but they cut startup times and memory allocation noise in
the profiler, making my profiling time more productive.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5726 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 20:48:16 +00:00
422d4ceeea
removed useless file - no need for tableRecalibration, right now everything is done in PairHMMIndelErrorModel
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5725 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 20:35:44 +00:00
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.
...
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.
...
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.
...
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.
...
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
...
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
kshakir
carneiro
rpoplin
corin
hanna
delangel
ebanks