9f867d77ca
no sort order
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subtle bug fixed.
2011-10-20 18:44:09 -04:00
c9d8b22092
Added BWASW support to the pipeline
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Data Processing Pipeline can now use BWASW for realigning the reads. Useful for Ion Torrent data.
2011-10-20 18:36:28 -04:00
093cd95c5d
Merged bug fix from Stable into Unstable
2011-10-20 17:03:22 -04:00
d7367c152a
Fixing 'revert' when not realigning
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RevertSam was reverting the alignment information and that was screwing up the pipeline if you didn't want to run it with BWA. Fixed.
2011-10-20 17:01:54 -04:00
ed402588cc
Adding the "gold standard NA12878" target
2011-10-20 16:19:13 -04:00
c27e2fb676
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-18 15:23:05 -04:00
e5fc828546
With Khalid's implicit approval, I have removed this line that overrides the memory limit of the VCF-gathering function, so that the inherited limit remains
2011-10-18 14:47:39 -04:00
0939d16a8d
String not empty bug
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Apparently var X: String = _ is not the same as var X: String = "". :(
2011-10-13 13:22:05 -04:00
66b5646f95
Adding hidden options to the DPP
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controlling the default platform parameter to Count Covariates and the number of scatter gather jobs to generate are now available under hidden parameters
2011-10-11 13:56:00 -04:00
73f9d1f217
GATK read group requirement iron hand
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-- The GATK will now throw a user exception if it opens a SAM/BAM file that doesn't have at least one RG defined
-- LIBS again throws an error if the complete list of samples isn't provided
-- Updating ExmpleCountLociPipeline test to use the well-formated versions of the exampleBAM and exampleFASTA files in testdata, instead of the old broken ones in validation_data.
-- Convenience constructors for UserExceptions.MalformedBAM
2011-10-06 08:40:35 -07:00
a91509e7dd
Shouldn't be public
2011-10-05 15:22:57 -07:00
84bd355690
Merged bug fix from Stable into Unstable
2011-09-27 14:34:39 -04:00
b090751f62
Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.
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Updates to HybridSelectionPipeline:
- Added annotations back via snpEff
- Minor updates to VQSR paths and lowered memory
2011-09-27 14:33:57 -04:00
77ba59e30a
Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-27 00:51:45 -04:00
648b959361
Minor change to log an info message when a signal such as Ctrl-C is caught.
2011-09-27 00:50:19 -04:00
d3cc25454c
Updating the MDCP
2011-09-22 11:27:40 -04:00
623c49765d
NO BAQ ON EXOMES!
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says the boss.
2011-09-22 11:13:40 -04:00
5d0f284305
Fixing exome specific arguments to the VQSR in the methods development calling pipeline
2011-09-21 20:26:28 -04:00
758ecf2d43
Bringing latest updates of ReduceReads to the master repository
2011-09-20 16:35:09 -04:00
08ffb18b96
Renaming datasets in the MDCP
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Making dataset names and files generated by the MDCP more uniform.
2011-09-20 11:02:51 -04:00
ba150570f3
Updating to use new rod system syntax plus name change for CountRODs
2011-09-19 13:30:32 -04:00
095f75ff7d
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-19 12:24:12 -04:00
85626e7a5d
We no longer want people to use the August 2010 Dindel calls for indel realignment but instead Guillermo's new whole genome bi-allelic indel calls; updating the bundle accordingly. Also, there was some confusion by the 1000G data processing folks as to exactly what these indel files are, so I've renamed them so that it's clear. Wiki updated too.
2011-09-19 12:24:05 -04:00
6ea57bf036
Merge branch 'master' into sgintervals
2011-09-19 09:50:19 -04:00
33967a4e0c
Fixed issue reported by chartl where cloned functions lost tags on @Inputs.
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Updated ExampleUnifiedGenotyper.scala with new syntax.
2011-09-16 12:46:07 -04:00
981b78ea50
Changing 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.
2011-09-12 12:17:43 -04:00
7f9000382e
Making indel calls default in the MDCP
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You can turn off indel calling by using -noIndels.
2011-09-09 14:09:26 -04:00
06cb20f2a5
Intermediate commit cleaning up scatter intervals
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-- Adding unit tests to ensure uniformity of intervals
2011-09-09 12:56:45 -04:00
510d5e7730
Merged bug fix from Stable into Unstable
2011-09-09 01:34:55 -04:00
367bbee25a
Fixed typo when printing the contents or last N lines of a file. Thanks to larryns.
2011-09-09 01:33:25 -04:00
ee9d599558
Just cleaning up
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clean up old commented code from tha data processing pipeline.
2011-09-07 13:32:40 -04:00
28d782b4c7
Allowing multiple dnsnp and indel files in the DPP
2011-09-02 13:38:47 -04:00
ad4ea0b80b
Merged bug fix from Stable into Unstable
2011-09-01 18:14:45 -04:00
e253f6f05d
Fixing typo in DPP
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platform and library were exchanged when rebuilding the read group information
2011-09-01 18:13:52 -04:00
d2a33beff7
Added WGS/WEX b37-decoy CEU trio datasets
2011-09-01 13:14:40 -04:00
61633c95a8
Default jobreport is now jobPrefix, so you see logs like Q-2508.jobreport.txt
2011-08-28 19:19:45 -04:00
b38de1fa35
Now captures the exechost in the job report
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-- Works for in process, shell, and LSF runners
-- Cleanup of debugging output
2011-08-28 12:05:56 -04:00
e37a638e09
Fix for disallowed characters in GATKReportTable
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-- Illegal characters are automatically replaced with _
2011-08-26 13:24:06 -04:00
0cb1605df0
Clean documentation for JobRunInfo
2011-08-26 09:22:58 -04:00
415d5d5301
LSF long times are in seconds, convert to milliseconds to meet standard
2011-08-26 09:18:28 -04:00
eef1ac415a
Merge branch 'master' into rodTesting
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Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
2011-08-26 00:35:41 -04:00
e03dfdb0ab
Automatic iteration field addition works properly.
2011-08-25 16:59:02 -04:00
e01273ca7c
Queue now writes out queueJobReport.pdf
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-- General purpose RScript executor in java (please use when invoking RScripts)
-- Removed groupName. This is now analysisName
-- Explicitly added capability to enable/disable individual QFunction
2011-08-25 16:57:11 -04:00
0f4be2c4a4
Argument to disable queueJobReport entirely
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-- Minor improvements to RodPerformanceGoals
2011-08-25 13:32:03 -04:00
d65faf509c
Default output name for Queue JobReport is queue_jobreport.gatkreport.txt
2011-08-25 13:15:20 -04:00
a7d6946b22
Refactored QJobReport and QFunction, which is now automatically tracked
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-- All QFunctions, including sg ones, are tracked
-- Removed memory information
2011-08-25 13:13:55 -04:00
16caca0822
BLASR BAMs and new BWA parameters
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*Added the functions to turn a BLASR generated BAM file into a usable BAM file.
*Modified the bwa parameters according to test results from NA12878 pb2k dataset.
2011-08-24 17:04:07 -04:00
e3f5d7067a
Added ReorderSam queue binding
2011-08-24 17:03:11 -04:00
08fb21f127
Removing hostname
2011-08-24 16:45:50 -04:00
dc8398e165
fixing bai output for indel cleaning.
2011-08-24 15:58:34 -04:00
Mauricio Carneiro
Menachem Fromer
Mark DePristo
Khalid Shakir
Ryan Poplin
Eric Banks