beb947d3cc
Standalone program to create an XML index of the GSA pipeline directory suitable for loading in IGV.
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This is a replacement for an ancient Perl script that will soon be retired.
2011-08-26 14:48:38 -04:00
5a6ae954bf
Added VCF streaming to tribbleVsGATK
2011-08-26 14:04:48 -04:00
bd92a1b220
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-26 13:24:26 -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
6e66f1c243
Removing code that cleans up the assembly graph for purposes of display. There seems to be bugs
2011-08-26 12:36:12 -04:00
8f150c6764
Assembly debug mode now uses smith-waterman to locally align all haplotypes and outputs to a bam file instead of first writing a fasta file and using bwa-sw outside of the GATK.
2011-08-26 10:43:40 -04:00
8f90a22555
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-26 10:16:56 -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
c11ddf3da3
Enchancements to queueJobReport
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-- Runtimes are in seconds, not milliseconds
-- Job names are shown in the gantt chart
-- axis names are clearer
-- documentation for all of the function
2011-08-26 09:17:09 -04:00
c0503283df
Spelling fix requires md5 updates
2011-08-26 07:40:44 -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
6bd3959ff2
Now shows job scheduling over time
2011-08-26 00:19:50 -04:00
34fb6ef798
SitesVsGenotypes should only be on chr1
2011-08-26 00:18:09 -04:00
c0e55c5ca4
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-25 22:42:27 -04:00
9b7512fd94
Just because there's a ref base doesn't mean the VC needs to be padded
2011-08-25 22:42:14 -04:00
6d8851eb63
Added option to control memory usage of DoC merging step
2011-08-25 22:12:54 -04:00
03a655023c
Must explicitly enable multithreaded tests
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-- Avoids sending nt 8 jobs to the unsuspecting farm
2011-08-25 19:41:08 -04:00
1a50a251d8
Draft version of report
2011-08-25 17:03:50 -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
09a729da3a
Removing incorrect comment
2011-08-25 15:42:52 -04:00
3eed5af2f7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-25 15:37:35 -04:00
8bbef79fc2
Create clipped alleles during allele parsing instead of creating a full VC, clipping alleles, and regenerating the VC from scratch.
2011-08-25 15:37:26 -04:00
c34b4b20aa
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-25 14:58:15 -04:00
6347317ba8
Too fast to commit last time
2011-08-25 14:58:10 -04:00
0f4be2c4a4
Argument to disable queueJobReport entirely
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-- Minor improvements to RodPerformanceGoals
2011-08-25 13:32:03 -04:00
999dff1252
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-25 13:28:23 -04:00
1bf0fcd7a4
Obvious bug fix in HSP script: not enough to fix test yet, though
2011-08-25 13:27:55 -04:00
d81122cf5f
Fixed up so that all modes can go through multiple iterations
2011-08-25 13:22:39 -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
08f6c3eea9
companion gantt charts for Q runtimes
2011-08-25 12:59:59 -04:00
e5ca61e371
Bug fix for multiallelic events in haplotype caller
2011-08-25 11:09:39 -04:00
5e0660e27d
Adding debug option to output all possible haplotypes in fasta format for use with bwa
2011-08-25 10:31:10 -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
d50474f14c
Merged bug fix from Stable into Unstable
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resolved conflicts by maintaining all the changes in UNSTABLE where this bug had already been fixed.
Conflicts:
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
2011-08-24 16:06:36 -04:00
dc8398e165
fixing bai output for indel cleaning.
2011-08-24 15:58:34 -04:00
da5e6b52e7
Refactoring the smith-waterman and genotyping-related pieces into their own engine
2011-08-24 15:54:17 -04:00
06e30a81d1
Fixes throughout for getting job information
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-- no more hostname -- it's just not going to be important
2011-08-24 15:30:09 -04:00
29c7b10f7b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-24 15:18:58 -04:00
e5008aba00
Output the top two haplotypes as a variant call by running smith-waterman alignment against the reference and calling any difference as variation. This is the first verion that runs end-to-end by taking in reads as bam file and writing out variant calls in VCF.
2011-08-24 15:18:44 -04:00
4918519a58
No more NPE in getRuntime() when you cntr-c out of Queue
2011-08-24 14:14:01 -04:00
16d8360592
QJobReport is now the official capability name
2011-08-24 13:59:14 -04:00
d047c19ad1
Writes output to file
2011-08-24 13:52:05 -04:00
61f5968807
Change indel/snp selection to new arguments
2011-08-24 13:42:23 -04:00
3ae68e2397
JobLogging trait now writes out GATKReport log of jobs
2011-08-24 13:36:39 -04:00
e618cb1e79
a) Renamed/expanded SelectVariants arguments that choose particular kinds of variants and particular allelic types, now instead of -Indels or -SNPs we can specify for example -selectType [MIXED|INDEL|SNP|MNP|SYMBOLIC]. To select biallelic, multiallelic variants, use -restrictAllelesTo [BIALLELIC|MULTIALLELIC]. Corresponding gatkdocs changes.
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b) More useful AC,AF logging in VariantsToTable with multiallelic sites: instead of logging comma-separated values, log max value by default. Hidden, experimental argument -logACSum to log sum of ACs instead. This is due to extreme slowness of R in parsing strings to tokens and computing max/sum itself (~100x slower than gatk).
c) Added integrationtest for new SelectVariants commands
2011-08-24 12:25:50 -04:00
David Roazen
Mark DePristo
Ryan Poplin
Eric Banks
Menachem Fromer
Guillermo del Angel
Mauricio Carneiro