c8c06c7753Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-02-11 23:02:19 -0500
ac9250b12bDon't assume chrom20, just pull from the file list
Eric Banks
2012-02-11 23:02:05 -0500
3caa1b83bbUpdating HC integration tests
Ryan Poplin
2012-02-11 11:48:32 -0500
9b8fd4c2ffUpdating the half of the code that makes use of the recalibration information to work with the new refactoring of the bqsr. Reverting the covariate interface change in the original bqsr because the error model enum was moved to a different class and didn't make sense any more.
Ryan Poplin
2012-02-11 10:57:20 -0500
f52f1f659fMultiallelic implementation of the TDT should be a pairwise list of values as per Mark Daly. Integration tests change because the count in the header is now A instead of 1.
Eric Banks
2012-02-10 14:15:59 -0500
f1990981fcA little BQSR scala script to use with scatter/gather
Mauricio Carneiro
2012-02-10 14:00:53 -0500
a7c6f255e9Adding the old gatherer to BQSR
Mauricio Carneiro
2012-02-10 13:33:57 -0500
1fb19a0f98Moving the covariates and shared functionality to public
Mauricio Carneiro
2012-02-10 11:43:48 -0500
48cc4b913abugfix for incremental refresh in gsafolkLSFlogs
Mark DePristo
2012-02-10 11:30:36 -0500
8ad4046642Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-02-10 11:18:02 -0500
0722df46dbgsafolkLSFLogs creates a subset of LSF MySQL db related to gsafolk only
Mark DePristo
2012-02-10 11:11:14 -0500
5e18020a5fMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-02-10 11:08:33 -0500
f53cd3de1bBased on Ryan's suggestion, there's a new contract for genotyping multiple alleles. Now the requester submits alleles in any arbitrary order - rankings aren't needed. If the Exact model decides that it needs to subset the alleles because too many were requested, it does so based on PL mass (in other words, I moved this code from the SNPGenotypeLikelihoodsCalculationModel to the Exact model). Now subsetting alleles is consistent.
Eric Banks
2012-02-10 11:07:32 -0500
5af373a3a1BQSR with indels integrated!
Mauricio Carneiro
2012-02-08 14:39:55 -0500
7a937dd1ebSeveral bug fixes to new genotyping strategy. Update integration tests for multi-allelic indels accordingly.
Eric Banks
2012-02-09 16:14:22 -0500
0f728a0604The Exact model now subsets the VC to the first N alleles when the VC contains more than the maximum number of alleles (instead of throwing it out completely as it did previously). [Perhaps the culling should be done by the UG engine? But theoretically the Exact model can be called outside of the UG and we'd still want the context subsetted.]
Eric Banks
2012-02-09 14:02:34 -0500
aa097a83d5Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Matt Hanna
2012-02-09 11:26:48 -0500
b57d4250bfDocumentation request by Eric. At each stage of the GATK where filtering occurs, added documentation suggesting the goal of the filtering along with examples of suggested inputs and outputs.
Matt Hanna
2012-02-09 11:24:52 -0500
5b3d875833Incorporating Mark's suggestions on the AnalyzeCovariates plots.
Ryan Poplin
2012-02-09 09:05:08 -0500
d561914d4fRevert "First implementation of GATKReportGatherer"
Mauricio Carneiro
2012-02-08 23:28:55 -0500
270b160d87Incorporating feedback from Mauricio on the plots
Ryan Poplin
2012-02-08 16:26:32 -0500
4316437a62Initial version of R script that will be called by new BQSR to replace the entire AnalyzeCovariates program
Ryan Poplin
2012-02-08 16:00:12 -0500
2f800b078cChanges to default behavior of UG: multi-allelic mode is always on; max number of alternate alleles to genotype is 3; alleles in the SNP model are ranked by their likelihood sum (Guillermo will do this for indels); SB is computed again.
Eric Banks
2012-02-08 15:27:16 -0500
51ac87b28cMerge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Matt Hanna
2012-02-08 08:43:55 -0500
5b58fe741aRetiring Picard customizations for async I/O and cleaning up parts of the code to use common Picard utilities I recently discovered.
Matt Hanna
2012-02-03 16:43:00 -0500
cda1e1b207Minor manual merge update for List class to Seq interface usage.
Khalid Shakir
2012-02-08 02:24:54 -0500
ef74363b1bMerged bug fix from Stable into Unstable
Khalid Shakir
2012-02-08 02:14:26 -0500
23e7f1bed9When an interval list specifies overlapping intervals merge them before scattering.
Khalid Shakir
2012-02-08 02:12:16 -0500
f30731f19bthese were not supposed to be committed. Pulling it out
Mauricio Carneiro
2012-02-07 21:38:39 -0500
337819e791disabling the test while we fix it
Mauricio Carneiro
2012-02-07 19:22:32 -0500
c0c676590bFirst implementation of GATKReportGatherer
Roger Zurawicki
2012-01-09 23:46:48 -0500
e89887cd8elaying groundwork to have insertions and deletions going through the system.
Mauricio Carneiro
2012-02-07 18:11:53 -0500
717cd4b912Document -L unmapped
Eric Banks
2012-02-07 13:30:54 -0500
718da7757eFixes to ValidateVariants as per GS post: ref base of mixed alleles were sometimes wrong, error print out of bad ACs was throwing a RuntimeException, don't validate ACs if there are no genotypes.
Eric Banks
2012-02-07 13:15:58 -0500
a6477e558aadding docs to HaplotypeCaller
Ryan Poplin
2012-02-07 09:37:32 -0500
9d1a19bbaaMulti-allelic indels were not being printed out correctly in VariantsToTable; fixed.
Eric Banks
2012-02-06 22:49:29 -0500
6e6f0f10e1BaseQualityScoreRecalibration walker (bqsr v2) first commit includes
Mauricio Carneiro
2012-02-06 12:31:20 -0500
0717c79901Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-02-06 16:23:36 -0500
91897f5fe7Transpose rows/cols in AF table to make it molten (so I can plot easily in R)
Eric Banks
2012-02-06 16:23:32 -0500
fb5786385cMerged bug fix from Stable into Unstable
Guillermo del Angel
2012-02-06 13:22:56 -0500
6ec686b877Complement to previous commit: make sure we also don't inherit filter from input VCF when genotyping at an empty site
Guillermo del Angel
2012-02-06 13:19:26 -0500
93ffca1e3aMerged bug fix from Stable into Unstable
Guillermo del Angel
2012-02-06 11:58:58 -0500
827be878b4Bug fix when running UG in GenotypeGivenAlleles mode: if an input site to genotype had no coverage, the output VCF had AC,AF and AN inherited from input VCF, which could have nothing to do with given BAM so numbers could be non-sensical. Now new vc has clear attributes instead of attributes inherited from input VCF.
Guillermo del Angel
2012-02-06 11:58:13 -0500
fbbd04621dMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-02-06 11:53:31 -0500
edb4edc08fCommented out unused metrics for now
Eric Banks
2012-02-06 11:53:15 -0500
096c23a473Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-02-06 11:10:38 -0500
dc05b71e39Updating Covariate interface with Mauricio to include an errorModel parameter. On the fly recalibration of base insertion and base deletion quals is live for the HaplotypeCaller
Ryan Poplin
2012-02-06 11:10:24 -0500
1e11408f8bMerged bug fix from Stable into Unstable
Guillermo del Angel
2012-02-06 10:34:26 -0500
090d87b48bBug fix in ValidationSiteSelector: when input vcf had genotypes and was multiallelic, the parsing of the AF/AC fields was wrong. Better logic to unify parsing of field
Guillermo del Angel
2012-02-06 10:33:12 -0500
9d94f310f1Break AF histogram into max and min AFs
Eric Banks
2012-02-06 09:01:19 -0500
b7ffd144e8Cleaning up the covariate classes and removing unused code from the bqsr optimizations in 2009.
Ryan Poplin
2012-02-06 08:54:42 -0500
cef550903eMinor optimization
Eric Banks
2012-02-06 00:48:00 -0500
5343f8ba67Initial version of on-the-fly, lazy loading base quality score recalibration. It isn't completely hooked up yet but I'm committing so Mauricio and Mark can see how I envision it will fit together. Look it over and give any feedback. With the exception of the Solid specific code we are very very close to being able to remove TableRecalibrationWalker from the code base and just replace it with PrintReads -BQSR recal.csv
Ryan Poplin
2012-02-05 13:09:03 -0500
2cd33b2f1fBetter display of LSF usage for gsafolk
Mark DePristo
2012-02-04 08:22:12 -0500
f94d547e97Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-02-03 17:14:20 -0500
894d3340beActive Region Traversal should use GATKSAMRecords everywhere instead of SAMRecords. misc cleanup.
Ryan Poplin
2012-02-03 17:13:52 -0500
4a57add6d0First implementation of DiagnoseTargets
Mauricio Carneiro
2012-02-01 19:35:33 -0500
3dd6a1f962Adding some generic sum and average functions to MathUtils
Mauricio Carneiro
2012-02-01 19:35:09 -0500
e1d69e4060make the size of a GenomeLoc int instead of long
Mauricio Carneiro
2012-02-01 19:34:39 -0500
92e3e5e565Merge branch 'master' of ssh://ni.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable
Christopher Hartl
2012-02-03 15:48:22 -0500
5af3999a2dupdating HaplotypeCaller integration tests
Ryan Poplin
2012-02-03 14:04:58 -0500
0e44430e47Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-02-03 13:45:11 -0500
aa3638ecb3Merge branch 'master' of ssh://chartl@ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Christopher Hartl
2012-02-03 13:42:09 -0500
53e6d66601analyzeRunReports pushes full stack trace to DB for reporting
Mark DePristo
2012-02-03 12:31:29 -0500
79da5ca2aeParses major and minor GATK versions now. Added unit tests
Mark DePristo
2012-02-03 09:50:26 -0500
3abfbcbcf2Generalized the TDT for multi-allelic events
Eric Banks
2012-02-03 12:23:21 -0500
601e53d633Fix when specifying preset active regions with -AR argument
Ryan Poplin
2012-02-02 16:34:26 -0500
974c2499ccBugfixed to script.
Christopher Hartl
2012-02-02 12:55:54 -0500
f596377e73Oops. Forgot that some samples are new and the data directory doesn't already exist. Now try to create it if it's not already present.
Eric Banks
2012-02-02 12:39:49 -0500
27ea6426a4Small script to chunk up a VCF into equal-sized chunks
Christopher Hartl
2012-02-02 12:29:03 -0500
0111505ea9Terrible. Swapping the paternal and sample ids.
Christopher Hartl
2012-02-02 11:41:16 -0500
0c562756ebAdd a memory limit so this thing doesn't get killed on the farm
Christopher Hartl
2012-02-02 10:30:09 -0500
1f50f6970bMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-02-02 10:17:13 -0500
4ed06801a7Updating HaplotypeCaller's HMM calc to use GOP as a function of the read instead of a function of the haplotype in preparation for IQSR
Ryan Poplin
2012-02-02 10:17:04 -0500
d1a1888d2fMerge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-02-02 09:58:22 -0500
48220700ebAdding lftp to the supported download protocols for the 1000G sync. Initial results look very good! Bringing down chrom11 and chrom20 files now.
Eric Banks
2012-02-02 09:58:03 -0500
45bf2562cc.
Christopher Hartl
2012-02-02 09:11:17 -0500
f8c5406084Add the ability to extract samples
Christopher Hartl
2012-02-02 09:06:39 -0500
8adfc79123Merged bug fix from Stable into Unstable
Matt Hanna
2012-02-01 16:07:41 -0500
30b937d2afFix bug discovered in FGTP branch in which BlockInputStream returns -1 in cases where some data could be read, but not all the data requested by the caller.
Matt Hanna
2012-02-01 16:06:22 -0500
2109122cddmerging branches
Ryan Poplin
2012-02-01 14:37:24 -0500
bc6abc94e9Bug fix for check of isMateUnmapped. Requires check of mate is mapped.
Ryan Poplin
2012-02-01 14:32:19 -0500
a46a29501bMarking unused code in HC for removal.
Ryan Poplin
2012-02-01 13:22:17 -0500
b567ed8793Use the right reference path :(
Christopher Hartl
2012-02-01 12:35:18 -0500
87a63d54d6fix the script!
Christopher Hartl
2012-02-01 12:05:29 -0500
810996cfcaIntroducing: VariantsToPed, the world's most annoying walker! And also a busted QScript to run it that I need Khalid's help debugging ( frownie face ). Note that VariantsToPed and PlinkSeq generate the same binary file (up to strand flips...thanks PlinkSeq), so I know it's working properly. Hooray!
Christopher Hartl
2012-02-01 10:39:03 -0500
25d943f706Merge branch 'master' of ssh://chartl@ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Christopher Hartl
2012-02-01 10:32:11 -0500
e8528bc526updating HaplotypeCaller integration tests
Ryan Poplin
2012-02-01 09:43:19 -0500
dc23265640Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-02-01 09:22:43 -0500
579627568eLimit to 3 ALT alleles
Menachem Fromer
2012-01-31 23:39:39 -0500
08c7c07f25Added the option of not compressing read names to ReduceReads
Mauricio Carneiro
2012-01-31 17:14:57 -0500
056b24ccd6Resolving merge conflicts with LocusIteratorByState
Ryan Poplin
2012-01-31 16:13:32 -0500
febc634557Changing PileupElement's isSoftClipped to isNextToSoftClip since soft clipped bases aren't actually added to pileups, oops. Removing the intrinsic clustered variants filter from the HaplotypeCaller
Ryan Poplin
2012-01-31 16:06:14 -0500
7f70612bebMerge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Matt Hanna
2012-01-31 11:59:25 -0500
a630db1703Oops...HierarchicalMicroScheduler was transforming any exception from the walker level into a ReviewedStingException. Thanks to Ryan for pointing this out.
Matt Hanna
2012-01-31 11:58:21 -0500
a7f5d26326No more synthetic reads starting/ending with deletions
Mauricio Carneiro
2012-01-31 11:17:05 -0500
2f2f039c37Better flow for byNegTrainingFraction
Mark DePristo
2012-01-31 10:49:46 -0500
Eric Banks
Ryan Poplin
Mauricio Carneiro
Mark DePristo
Matt Hanna
Khalid Shakir
Roger Zurawicki
Guillermo del Angel
Christopher Hartl
Menachem Fromer