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Author SHA1 Message Date
rpoplin a13cbe1df0 The refactored recalibrator now passes the integration tests as well as my own validation tests. I'm ready to have other people start jamming on the files. I'll make an updated wiki page soon. The refactored recalibrator is currently a bit slower than the old one but there were a lot of great, easy ideas today for how to improve it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2013 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 22:20:06 +00:00
hanna 2cf9670d1e Allow users to directly specify filters from the command-line, applicable to 
any walker.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2012 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 18:40:16 +00:00
ebanks 6a37090529 Output changes for VCF and UG: 
1. Don't cap q-scores at 99
2. Scale SLOD to allow more resolution in the output
3. UG outputs weighted allele balance (AB) and on-off genotype (OO) info fields for het genotype calls (works for joint estimation model and SSG)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2011 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 16:31:31 +00:00
rpoplin 1e7ddd2d9f Added a validateOldRecalibrator option to CovariateCounterWalker which reorders the output to match the old recalibrator exactly. This facilitates direct comparison of output. Changed the -cov argument slightly to require the user to specify both ReadGroupCovariate and QualityScoreCovariate to make it more clear to the user which covariates are being used. Some speed up improvements throughout. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2010 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 15:55:56 +00:00
depristo 7e30fe230a oops, missing file 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2009 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 13:25:18 +00:00
depristo d316cbad4c VariantFilteration now accepts a VCF rod in addition to an input geli. It will then annotate this VCF file with filtering information in the INFO field too. --OnlyAnnotate will not write in filtering output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2008 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 13:24:58 +00:00
aaron f9819d5f13 a little clean-up 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2007 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 06:18:34 +00:00
aaron 2ed423ed56 print the current location in read walkers (in addition to the number of reads processed), along with some refactoring to support the change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2006 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 05:57:01 +00:00
ebanks c9c3cf477a Based on feedback from Kiran, we know uniquify sample names as sample.rodName (instead of sample.1, sample.2, ...) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2005 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 02:41:37 +00:00
ebanks 2fa2ae43ec Enough people have found this useful, so... 
Moving Callset Concordance tool to core and adding integration test.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2003 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 20:59:18 +00:00
ebanks 3793519bd4 -Added convenience method to VCF record to tell if it's a no call and have rodVCF use it before querying for info fields 
-Don't restrict info fields to 2-letter keys
[about to move these to core]


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2002 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 20:52:51 +00:00
rpoplin 740a5484c4 Added some documentation to the code, mostly especially to CovariateCounterWalker but various comments added throughout. Also changed the HashMap data structure to accept an estimated initial capacity. This had a very modest improvement to the speed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2001 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 20:13:56 +00:00
ebanks 74751a8ed3 -Some minor fixes to get accurate vcf record merging done 
-Improvement to snp genotype concordance test

And with that, it looks like I get revision #2000.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2000 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 06:40:55 +00:00
ebanks ab705565cf Completely refactored the Callset Concordance code. Now, it takes in VCF rods and emits a single VCF file which has merged calls from all inputs and is annotated (in the INFO fields) with the appropriate concordance test(s). 
Still needs a bit of polish...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1999 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 05:03:13 +00:00
ebanks bc6f24e88f Added VCFUtils which contains some useful VCF-related functions (e.g. ability to merge VCF records). 
Also, various minor improvements.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1998 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 04:53:32 +00:00
ebanks cff645e98b convenience method to deal with genotypes that are unsorted (e.g. CA vs. AC) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1997 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 04:45:49 +00:00
kiran 7fde6c0bf4 One more output tweak. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1996 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 04:42:55 +00:00
kiran 00a7113d7a Tweaks to formatting of output table. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1995 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 04:33:36 +00:00
ebanks 7ce0df76f8 Added accessors to the rod data sources so that walkers can access the name/file/type triplets for input rods. This is necessary if e.g. you want to create a vcf writer based on all of the samples being input. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1994 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 04:25:39 +00:00
ebanks d07f3bb6f6 Added methods to get strand bias and to test if record has allele freq or bias fields set. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1993 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 04:20:35 +00:00
kiran 3313b0ddb4 Fixed a minor bug where the lodThreshold wasn't being printed in the header. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1992 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-08 16:51:36 +00:00
kiran 95d381efe2 Optionally computes the error rate using the best base and a random base. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1991 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-08 16:47:34 +00:00
kiran 567f5758d2 Optionally lists read depths by read group. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1990 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-08 16:39:19 +00:00
kiran a679bdde18 FindContaminatingReadGroupsWalker lists read groups in a single-sample BAM file that appear to be contaminants by searching for evidence of systematic underperformance at likely homozygous-variant sites. 
Procedure:
1. Sites that are likely homozygous-variant but are called as heterozygous are identified.
2. For each site and read group, we compute the proportion of bases in the pileup supporting an alternate allele.
3. A one-sample, left-tailed t-test is performed with the null hypothesis being that the alternate allele distribution has a mean of 0.95 and the alternate hypothesis being that the true mean is statistically significantly less than expected (pValue < 1e-9).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1989 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-08 16:36:39 +00:00
kiran 2225d8176e A convenience class for maintaining a dynamically growing table of values with access to the elements by named row and column identifiers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1988 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-08 16:34:35 +00:00
hanna 21c5f543fa Fix sharding bug -- loci to which >100,000 (= 1 shard) reads are assigned an 
alignment start will confuse the sharding system and cause it to return duplicate reads.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1987 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-08 14:27:26 +00:00
rpoplin 84ba604611 Sequential quality score calculation is now in place in the refactored recalibrator and matches the quality scores calculated by the old recalibrator exactly; at least on the small sets of data used so far. Validation, documentation, and optimization work is on going. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1985 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-07 15:55:16 +00:00
depristo bf1bc94060 Fixes for PooledConcordance bugs and lack of safety checking 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1984 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-07 01:54:10 +00:00
rpoplin 66d4a995e6 Initial check in of refactored Recalibrator. The new walkers are called CountCovariatesRefactored and TableRecalibrationRefactored. More work is needed to finish up the sequential calculation and to document the code sufficiently. These files are not ready to be used by other people quite yet. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1982 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-06 22:33:55 +00:00
ebanks 6fdfc97db6 Added optional field DP to VCF output for Mark. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1981 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-06 20:03:22 +00:00
ebanks 0a55fa5bb1 Completely refactored the Genotype Concordance module(s). 
Now PooledConcordance and GenotypeConcordance inherit from the same super class (and can therefore share data structures and functionality).  Also, they now use ConcordanceTruthTable to keep track of necessary info.
GenotypeConcordance passes integration tests.
PooledConcordance needs to be finished by Chris.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1979 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-06 16:27:16 +00:00
ebanks d549347f25 Refactored GenotypeLikelihoods to use an underlying 4-base model. 
It needs to be modified a bit and then hooked up to a pooled model, but that is now possible.
At this point, there is no difference to the Unified Genotyper.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1978 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-05 21:59:25 +00:00
jmaguire 4d3871c655 don't flush anymore. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1977 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-05 19:11:51 +00:00
aaron aacd72854f a fix for a bug Andrey discovered: in read-based interval traversals we're dupplicating reads in rare cases. The problem was that to accomidate a bug in SAM JDK indexing, we were forced to add one to the stop of our QueryOverlapping() calls to ensure we always got all of the overlapping reads. 
Added a PlusOneFixIterator that wraps other iterators, and eliminates reads that start outside of our intended interval (interval stop - 1).  Updated and checked BamToFastqIntegrationTest MD5 sums.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1976 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-05 05:26:33 +00:00
hanna 43c3ee61d5 Fix minor mapping quality bug. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1973 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-04 14:33:23 +00:00
ebanks a545859c62 Joint Estimation model now emits a reasonable slod 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1969 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 21:12:42 +00:00
ebanks 11d950abe0 No longer allow the lod_threshold argument - use confidence instead. 
Have UG output qscores in all cases.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1968 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 16:18:51 +00:00
asivache 2fb45dbd73 Make window size a command line argument 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1967 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 16:13:35 +00:00
asivache 55f61b1f88 Bug fix in adjustment of the shift position. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1966 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 16:08:11 +00:00
depristo 5d5dc989e7 improvements to VCF and variant eval support of VCF -- now listens to the filter field 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1963 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 12:09:30 +00:00
hanna c63af32fc7 The BWA/C bindings were triggering the local aligner to repeatedly reload the 
ref genome.  Make sure the reference genome is cached.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1961 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 00:01:55 +00:00
ebanks 3a33401822 2nd stage of the genotyper output refactoring is complete. 
Now, all output is generalized and all of the intelligence lies where it is supposed to.
Next stage is syncing up old and new models and making sure we're outputting exactly what we should.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1960 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-02 22:43:08 +00:00
aaron ba67c7f02b added a warning for those using bed files; we properly convert bed to the internal representation but the user needs to be aware that any output will be one-based closed intervals 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1959 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-02 21:09:18 +00:00
aaron b71b66bd88 the underlying parameter is a float so we need to use Float.valueOf() instead; Noticed by external user Hou Huabin 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1958 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-02 20:22:25 +00:00
hanna 5a510e6d98 New PackageUtils interferes with the packaging utility. Revert until Aaron and 
I can get together to make this work.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1957 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-02 19:14:14 +00:00
aaron de6ae51f7e Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar. 
A couple of notes:
-Commented out BaseTransitionTableCalculator.scala because it's won't build; Chris could you fix this one (or kill it if it's not needed).
-Removed the PrintReadsScala walker; moved the code over to a ScalaCountLoci walker (which is what the code was really doing).
-Added configurations items to the ivy xml file.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1956 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-02 06:02:41 +00:00
hanna 1896f334d9 Fixed collection of bugs in reads aligning to multiple locations. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1955 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-02 04:02:09 +00:00
ebanks af6d0003f8 -Generalized the GenotypeConcordance module to deal with any number of individuals (although it will default to its old behavior if the -samples argument is left out). 
-Make rods return the appropriate type of Genotype calls from getGenotype().



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1954 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-01 05:35:47 +00:00
hanna b95165e39c Make alignment (temporarily) part of main GenomeAnalysisTK.jar. Add some extra logging errors on failure. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1953 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-01 00:33:18 +00:00
asivache 4b0796ba58 After fixing a few glitches and bugs, this version finally works as intended 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1952 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-31 04:59:58 +00:00