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
f19862a643
Fixing conflicts.
2011-07-14 17:13:31 -04:00
43c6a8565b
looks better now.
2011-07-14 17:10:44 -04:00
09ffe277ae
Added a qscripts util package with some utility functions commonly shared across queue scripts. Refactored some of my public scripts to use it in an effort to make queue scripts more reusable and "supportable".
2011-07-14 17:09:35 -04:00
4f8230c750
Merged bug fix from Stable into Unstable
2011-07-14 16:44:57 -04:00
9f5180ab05
Recalibrates a list of bam files allowing multiple bams to be recalibrated out of a single 'mother' queue job.
2011-07-14 16:42:17 -04:00
df996a1a73
more progress report for the Data Processing Pipeline.
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Bam lists can now have empty lines, comments and whitespaces anywhere.
2011-07-13 14:53:58 -04:00
ff4e31c554
Changing the file names as per Kris request.
2011-07-13 12:59:18 -04:00
5298e3a942
Making the outputDir optional. Default = ./
2011-07-05 16:30:41 -04:00
7d3dfdfdf2
Updating the MDCP to use the classpath for the GATK jar, removing -gatk parameter.
2011-07-05 16:30:10 -04:00
b0fb63e20a
moving the example scala scripts to the qscripts package.
2011-07-01 16:14:59 -04:00
d19351f71a
Added capability of running multiple bam files in the same directory.
2011-07-01 16:02:28 -04:00
197b7141c1
Added an optional argument -bt <num_threads> for BWA to run multithreaded.
2011-06-30 14:41:57 -04:00
f4463d38ca
BWA requires pair ended reads to be sorted by read names when operating over BAM files, but Picard sorts by coordinate, so in case we use BWA in pair ended reads, the pipeline now resorts the BAM in read name order, realigns it then sorts it in coordinate order.
2011-06-30 14:29:21 -04:00
efd99c3c11
new home for the core qscripts
2011-06-30 11:32:06 -04:00
Mauricio Carneiro
Ryan Poplin
Khalid Shakir