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
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
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
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
dc8398e165
fixing bai output for indel cleaning.
2011-08-24 15:58:34 -04:00
cd12f7f286
Fixed list dependency
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Instead of creating a bam list file, I dynamically create a scala list and pass as parameters. This way the intermediate bam files don't get deleted before they should.
2011-08-24 11:12:46 -04:00
219252a566
Adapting to the new RodBinding framework
2011-08-24 11:12:46 -04:00
136f0eb685
Creating sample-bam list instead of joining
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This should save us at least one day in the trio decoy processing.
2011-08-22 18:03:39 -04:00
04d8bcaf19
Fixed bai removal on picard tools
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BAM index files were not being deleted because picard replaces the name of the file with bai instead of appending to it.
2011-08-22 18:03:39 -04:00
caebc88e9a
Consensus mode and new RodBinding framework.
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The DPP was not using the parameter correctly. It didn't matter for the default option (which is the only one we have been testing) but it would not work for knowns only or smith waterman. It is fixed now.
It now complies with the new rod binding framework.
2011-08-22 18:03:39 -04:00
f93a554b01
updating exome specific parameters in MDCP
2011-08-21 10:25:36 -04:00
b008676878
fixing the previous fix
2011-08-20 21:21:55 -04:00
539e157ecd
Fixing misc parameters in MDCP. The pipeline now does VariantEval of output by default. Fix for NaN vqslod values in VQSR
2011-08-20 11:28:48 -04:00
ddb5045e14
Updating the methods development calling pipeline for the new rod binding syntax and the new best practices.
2011-08-19 19:29:51 -04:00
b0ff5b1ff7
a better name for the pacbio processing pipeline
2011-08-10 16:16:53 -04:00
481630da00
BWA parameters added
2011-08-09 17:05:24 -04:00
22d2563823
added BWA SW alignment
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The pipeline now accepts fasta/fastq files and aligns them using BWA SW, adds default basequalities, creates read groups and performs BQSR.
2011-08-09 17:05:24 -04:00
bd1cf4c7bc
Pacbio Pipeline
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Added the base quality "filling" step to allow the pipeline to handle raw pacbio BAM files. This is the first step towards a generic pacbio data processing pipeline.
2011-08-09 17:05:24 -04:00
8072bd9831
Updating resource bundle generation qscript for changeover to git
2011-08-08 12:35:39 -04:00
2fd101135c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-08 10:49:43 -04:00
4d6cb33612
removing temporary bam index
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The clean bai file was left behind after the data processing pipeline was done
2011-08-08 10:49:28 -04:00
21dc9a5543
Adding mills/devine indel dataset to the resource bundle
2011-08-04 12:31:28 -04:00
aff681e407
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-04 11:05:25 -04:00
23ec5b94cf
fixed a missing check for null
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There was a missed check for the case when you don't provide an indels vcf for the cleaner.
2011-08-04 09:50:02 -04:00
8981367307
Updating memory usage for picard programs
2011-08-03 15:48:28 -04:00
a587f38808
Fixed example unified genotyper pipeline to wrap filter expressions with quotes and use rod binding name "variant" instead of "vcf".
2011-08-03 02:21:01 -04:00
2d94037ad0
Remove temporary index files (*.bai)
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some temporary index files were not being removed.
2011-07-30 02:05:22 -04:00
dcf21f379a
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-23 12:59:53 -04:00
f0a6dd27a1
Renaming the plot output directory names.
2011-07-23 12:59:37 -04:00
4f78025b0b
Merged bug fix from Stable into Unstable
2011-07-22 14:42:04 -04:00
4080e2cd88
* Added the decoy reference to the bundle under the b37 resources.
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* Updated the -svn argument to -ver since we don't use svn anymore (also updated the wiki).
2011-07-22 14:41:22 -04:00
9ad5c7dfa4
Resolving simple conflicts in the data processing pipeline.
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Conflicts:
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
2011-07-19 08:05:11 -04:00
7688bda1a6
better progress report for the DPP
2011-07-18 23:39:47 -04:00
2b465ab43b
* added optional 'no validation' for the Data Processing pipeline.
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* some simplifications on the picard classes
2011-07-18 23:30:31 -04:00
4cf7a2af23
Removed broad specific default paths so people from outside the broad can use it.
2011-07-18 23:25:21 -04:00
5cb5a4ec75
Merged bug fix from Stable into Unstable
2011-07-16 00:23:59 -04:00
dd92a14b40
Made extra indel VCF optional but DBSNP mandatory.
2011-07-16 00:23:35 -04:00
2fa5dbb0fe
Merged bug fix from Stable into Unstable
2011-07-16 00:15:19 -04:00
ed55182a4c
Removing Broad specific paths from parameters and making them required. This should make it unambiguous for people inside and outside the Broad to use the DataProcessingPipeline (as per request in the GetSatisfaction)
2011-07-16 00:09:00 -04:00
43bd45fcad
Merged bug fix from Stable into Unstable
2011-07-15 19:40:02 -04:00
fd1df31ef0
changing the output directory names for Analyze Covariates
2011-07-15 19:39:42 -04:00
aa30f416a3
Resolving conflicts
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Conflicts:
private/scala/qscript/depristo/ExomePostQCEval.scala
private/scala/qscript/depristo/PostCallingQC.scala
private/scala/qscript/org/broadinstitute/sting/queue/qscripts/archive/ExomePostQCEval.scala
2011-07-15 16:21:42 -04:00
7b7d40d5d9
A better name for the qscript utilities. Throw here every method you find yourself repeatedly implementing in your qscripts!
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Refactoring appropriately.
2011-07-15 14:34:50 -04:00
a670d6420a
Refactoring Qscript utils into queue general utils package.
2011-07-15 14:31:43 -04:00
Eric Banks
Khalid Shakir
Ryan Poplin
Mauricio Carneiro