6bd42c053dMerge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Mark DePristo
2011-09-18 20:18:39 -0400
bed78b47e0Marginally better formating, with hours the default time
Mark DePristo
2011-09-18 20:18:18 -0400
091c7197cdFixed memory leak and bug with deletions in clipping
Roger Zurawicki
2011-09-18 19:21:51 -0400
67cca5196cMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2011-09-18 12:13:01 -0400
cb4a50b147Adding ability to try both small and large kmer lengths. Highest likelihood wins.
Ryan Poplin
2011-09-17 16:42:49 -0400
7fa1e237d9Forgot to git stash pop new MD5's for CombineVariants integration test
Guillermo del Angel
2011-09-16 12:53:54 -0400
e7b9a009b7Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2011-09-16 12:48:30 -0400
42f3b7ba32Merged bug fix from Stable into Unstable
Khalid Shakir
2011-09-16 12:46:38 -0400
33967a4e0cFixed issue reported by chartl where cloned functions lost tags on @Inputs. Updated ExampleUnifiedGenotyper.scala with new syntax.
Khalid Shakir
2011-09-16 12:46:07 -0400
92f7db3228Can now optionally suppress the use of all annotations and then add back in specific annotations/groups. This was necessary, since using all annotations for VariantAnnotator NOW includes SNPeff, which (annoyingly) requires a SNPeff VCF...
Menachem Fromer
2011-09-16 02:40:24 -0400
b2e8e11128Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Menachem Fromer
2011-09-16 00:52:27 -0400
3cd9f3fe81Merge remote-tracking branch 'unstable/master'
Eric Banks
2011-09-15 21:14:17 -0400
57b3efa2e2Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Christopher Hartl
2011-09-15 21:06:38 -0400
939babc820Updating formating for ValidationAmplicons GATK docs
Christopher Hartl
2011-09-15 21:05:51 -0400
9fdf1f8eb6Fix some doc formatting for Depth of Coverage
Christopher Hartl
2011-09-15 21:05:22 -0400
e6e9b08c9aMust provide alleles VCF to UGCallVariants
Menachem Fromer
2011-09-15 18:51:09 -0400
1960bcabb8Updated to use new ROD-binding system
Menachem Fromer
2011-09-15 18:07:32 -0400
d78e00e5b2Renaming VariantAnnotator SnpEff keys
David Roazen
2011-09-15 16:09:07 -0400
1971fb35d7Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2011-09-15 16:55:33 -0400
9dc6354130Oops didn't mean to touch this test before
Eric Banks
2011-09-15 16:55:24 -0400
2a8b8efd2fMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2011-09-15 16:26:35 -0400
2f58fdb369Adding expected output doc to CountCovariates
Ryan Poplin
2011-09-15 16:26:11 -0400
fd1831b4a5Updating docs to include more details
Eric Banks
2011-09-15 16:25:03 -0400
6d02a34bfbUpdating docs to include output
Eric Banks
2011-09-15 16:17:54 -0400
4ef6a4598cUpdating docs to include output
Eric Banks
2011-09-15 16:10:34 -0400
fe474b77f8Updating docs so printing looks nicer
Eric Banks
2011-09-15 16:05:39 -0400
f04e51c6c2Adding docs from Andrey since his repo was all screwed up.
Eric Banks
2011-09-15 15:38:56 -0400
ce73dc4071Update to the bindings for liftOverVCF.pl (to -V from -B)
Christopher Hartl
2011-09-15 15:33:09 -0400
7d6b34b1bbCan now optionally annotate with a dbSNP VCF
Menachem Fromer
2011-09-15 15:31:38 -0400
86480b2e13Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2011-09-15 15:31:07 -0400
04f5723399Updated to use new ROD-binding system
Menachem Fromer
2011-09-15 14:28:06 -0400
d369d10593Adding documentation before the release for GATK wiki page
Eric Banks
2011-09-15 13:56:23 -0400
202405b1a1Updating the FunctionalClass stratification in VariantEval to handle the snpEff annotations; this change really needs to be in before the release so that the pipeline can output semi-meaningful plots. This commit maintains backwards compatibility with the crappy Genomic Annotator output. However, I did clean up the code a bit so that we now use an Enum instead of hard-coded values (so it's now much easier to change things if we choose to do so in the future). I do not see this as the final commit on this topic - I think we need to make some changes to the snpEff annotator to preferentially choose certain annotations within effect classes; Mark, let's chat about this for a bit when you get back next week. Also, for the record, I should be blamed for David's temporary commit the other day because I gave him the green light (since when do you care about backwards compatibility anyways?). In any case, at least now we have something that works for both the old and new annotations.
Eric Banks
2011-09-15 13:52:31 -0400
1e682deb26Minor html-formatting-related documentation fix to the SnpEff class.
David Roazen
2011-09-15 13:07:50 -0400
a942fa38efRefine the way we merge records in CombineVariants of different types. As of before, two records of different types were not combined and were kept separate. This is still the case, except when the alleles of one record are a strict subset of alleles of another record. For example, a SNP with alleles {A*,T} and a mixed record with alleles {A*,T, AAT} are now combined when start position matches.
Guillermo del Angel
2011-09-15 10:22:28 -0400
3db457ed01Revert "Modified VariantEval FunctionalClass stratification to remove hardcoded GenomicAnnotator keynames"
David Roazen
2011-09-14 10:47:28 -0400
e0c8c0ddcbModified VariantEval FunctionalClass stratification to remove hardcoded GenomicAnnotator keynames
David Roazen
2011-09-14 06:04:32 -0400
1213b2f8c6SnpEff 2.0.2 support
David Roazen
2011-09-09 16:10:30 -0400
5b1bf6e244Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2011-09-13 17:04:43 -0400
c6672f2397Intermediate (but necessary) fix for Beagle walkers: if a marker is absent in the Beagle output files, but present in the input vcf, there's no reason why it should be omitted in the output vcf. Rather, the vc is written as is from the input vcf
Guillermo del Angel
2011-09-13 16:57:37 -0400
edf29d0616Explicit info message about uploading S3 log
Mark DePristo
2011-09-12 22:16:52 -0400
64df3950c1Emit minimalTable that can be read into R
Mark DePristo
2011-09-12 22:03:13 -0400
2316b6aad3Trying to fix problems with S3 uploading behind firewalls
Mark DePristo
2011-09-12 22:02:42 -0400
64707c33bbMerged bug fix from Stable into Unstable
Matt Hanna
2011-09-12 21:54:11 -0400
e63d9d8f8eMauricio pointed out to me that dynamic merging the unmapped regions of multiple BAMs ('-L unmapped' with a BAM list) was completely broken. Sorry about this! Fixed.
Matt Hanna
2011-09-12 21:50:59 -0400
4e116760f4Removing some old cruft from the packages dir. Updating AnalyzeCovariates to include all Covariates.
Eric Banks
2011-09-12 15:09:25 -0400
ec4b30de6dPatch from Laurent: typo leads to bad error messages.
Eric Banks
2011-09-12 14:45:53 -0400
9d9d438bc4New VariantAnnotatorEngine capability: an initialize() method for all annotation classes.
David Roazen
2011-09-12 12:28:23 -0400
981b78ea50Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts.
Ryan Poplin
2011-09-12 12:17:43 -0400
60ebe68affFixing issue in VariantEval in which insertion and deletion events weren't treated symmetrically. Added new option to require strict allele matching.
Ryan Poplin
2011-09-12 09:43:23 -0400
07d365ce39Fixing units in queue job report Gantt plots
Ryan Poplin
2011-09-12 09:01:34 -0400
09050a01dbAdding qscript to run the HaplotypeCaller in parallel
Ryan Poplin
2011-09-11 22:53:40 -0400
9a6b1f2681Fixed bug where exome could not output after contig change
Roger Zurawicki
2011-09-11 21:56:30 -0400
30be6d8bd6Removing the copy of the original assembler since it has been successfully assimilated
Ryan Poplin
2011-09-11 21:00:27 -0400
9344938360Uncomment code to add deleted bases covering an indel to per-sample genotype reporting, update integration tests accordingly
Guillermo del Angel
2011-09-10 19:41:01 -0400
b399424a9cFix integration test affected by non-calling all-zero PL samples, and add a more complicated multi-sample integration test from a phase 1 case, GBR with mixed technologies and complex input alleles
Guillermo del Angel
2011-09-09 20:44:47 -0400
e95d484757Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2011-09-09 18:31:14 -0400
a807205fc3a) Minor optimization to softMax() computation to avoid redundant operations, results in about 5-10% increase in speed in indel calling. b) Added (but left commented out since it may affect integration tests and to isolate commits) fix to per-sample DP reporting, so that deletions are included in count. c) Bug fix to avoid having non-reference genotypes assigned to samples with PL=0,0,0. Correct behavior should be to no-call these samples, and to ignore these samples when computing AC distribution since their likelihoods are not informative.
Guillermo del Angel
2011-09-09 18:00:23 -0400
72536e5d6dDone
Mark DePristo
2011-09-09 15:44:47 -0400
3c8445b934Performance bugfix for GenomeLoc.hashcode
Mark DePristo
2011-09-09 14:25:37 -0400
c6436ee5f0Whitespace cleanup
Mark DePristo
2011-09-09 14:24:29 -0400
87dc5cfb24Whitespace cleanup
Mark DePristo
2011-09-09 14:23:13 -0400
7f9000382eMaking indel calls default in the MDCP
Mauricio Carneiro
2011-09-09 14:09:11 -0400
1953edcd2dupdating Validate Variants deletion integration test
Ryan Poplin
2011-09-09 13:39:08 -0400
9ada9b3ed4Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2011-09-09 13:15:36 -0400
354529bff3adding Validate Variants integration test with a deletion
Ryan Poplin
2011-09-09 13:15:24 -0400
91c949db74Fixing ValidateVariants so that it validates deletion records. Fixing GATKdocs.
Ryan Poplin
2011-09-09 12:57:14 -0400
06cb20f2a5Intermediate commit cleaning up scatter intervals
Mark DePristo
2011-09-09 12:56:45 -0400
6bd8a53efdFix nasty bug involving the build report generation when multiple test targets are specified on the same command line.
David Roazen
2011-09-09 12:04:41 -0400
60a3618845Added "alltests" build targets.
David Roazen
2011-09-09 11:45:57 -0400
51eb95d638Missed these tests before
Eric Banks
2011-09-09 11:46:37 -0400
b318fcba35Added ability to profile the VCF output system too. Also, don't make the index test required.
Eric Banks
2011-09-09 11:13:11 -0400
6ad8943ca0CompOverlap no longer keeps track of the number of comp sites since it wasn't (and cannot) keeping track of them correctly.
Eric Banks
2011-09-09 09:45:24 -0400
510d5e7730Merged bug fix from Stable into Unstable
Khalid Shakir
2011-09-09 01:34:55 -0400
367bbee25aFixed typo when printing the contents or last N lines of a file. Thanks to larryns.
Khalid Shakir
2011-09-09 01:33:25 -0400
7fefc224baUnify outputs from PostCallingQC script to produce results compatible with the QC database building process.
Matt Hanna
2011-09-08 16:31:04 -0400
507574b1c8Merge branch 'cancer'
Mark DePristo
2011-09-08 16:10:02 -0400
61bccb71c6Improvements to AssignSomaticStatus
Mark DePristo
2011-09-08 16:09:33 -0400
388c9a9c55Enable public-only tests.
David Roazen
2011-09-02 14:34:31 -0400
48461b34afAdded TYPE argument to print out VariantType
Mark DePristo
2011-09-08 15:01:13 -0400
eaaba6eb51Confirming that when stratifying by sample in VE the monomorphic sites for a given sample are not counted for the relevant metrics. Adding integration test to cover it.
Eric Banks
2011-09-08 13:17:34 -0400
c204a08319Merge branch 'cancer'
Mark DePristo
2011-09-08 13:10:37 -0400
beabb67669Working version of AssignSomaticStatus
Mark DePristo
2011-09-08 13:09:26 -0400
5edc8f8578Moved to private package (intended home)
Mark DePristo
2011-09-08 11:54:55 -0400
7557f4a03aAssignSomaticStatus, now with the correct mathematical model
Mark DePristo
2011-09-08 11:54:14 -0400
2636d216deAdding indel vqsr integration test
Ryan Poplin
2011-09-08 10:38:13 -0400
9cba1019c8Another fix for genotype given alleles for indels. Expanding the indel integration tests to include multiallelics and indel records that overlap
Ryan Poplin
2011-09-08 09:25:13 -0400
e0020b2b29Fixing PrintRODs. Now has input and only prints out one copy of each record
Ryan Poplin
2011-09-08 08:58:37 -0400
6e6bf796d5first version of somatic detector
Mark DePristo
2011-09-08 08:46:38 -0400
29c968ab60clean up
Ryan Poplin
2011-09-08 08:42:43 -0400
59841f8232Fixing genotype given alleles for indels. Only take the records that start at this locus.
Ryan Poplin
2011-09-08 08:41:16 -0400
cd2c511c4aGCF improvements
Mark DePristo
2011-09-07 23:28:46 -0400
fe5724b6eaRefactored indexing part of StandardVCFWriter into superclass
Mark DePristo
2011-09-07 23:27:08 -0400
7f9047aec1updating parameters in assembler to decrease runtime
Ryan Poplin
2011-09-07 20:35:08 -0400
7ba6c29d32Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2011-09-07 19:18:24 -0400
0e8536f5f3Adding the ability to add multiple kmer lengths in the debruijn graph.
Ryan Poplin
2011-09-07 19:17:45 -0400
01b6177ce1Renaming GVCF -> GCF
Mark DePristo
2011-09-07 17:10:56 -0400
b220ed0d75Merge branch 'master' into rodrewrite
Mark DePristo
2011-09-07 17:05:35 -0400
45d54f6258Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2011-09-07 16:49:49 -0400
Mark DePristo
Roger Zurawicki
Ryan Poplin
Guillermo del Angel
Khalid Shakir
Menachem Fromer
Eric Banks
Christopher Hartl
David Roazen
Matt Hanna
Mauricio Carneiro