ef56b48eef
Add CNV sub-dir
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5928 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-02 21:47:13 +00:00
b4af28c7df
Handle case where -L argument (intervals) not given
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5886 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 20:24:56 +00:00
bc4305c956
Added memory limit parameter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5855 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 21:11:44 +00:00
833dff658a
Small script to do full variant annotation in parallel
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5853 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 20:33:20 +00:00
f3e94ef2be
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.
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JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar.
JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar.
Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath.
Walkers from the GATK package are now also embedded into the Queue package.
Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP.
Removed the GATK jar argument from the example QScripts.
Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts:
1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers.
2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3
Removed other unused code.
Re-fixed dry run function ordering.
Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-24 14:03:51 +00:00
0b45de14ed
Some minor updates to fully utilize the functionality of reduceByInterval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5411 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-09 20:38:08 +00:00
d6e3f2eba6
Added GC content calculator for CNV data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5240 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-14 22:29:55 +00:00
cdf53188d6
Updated DoC to work with scatter-gather; and, also manually implemented scatter-gather by sample above the scatter-gather by interval. Thansk to Khalid for his support!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5231 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-11 19:14:42 +00:00
947cc44854
Thanks to Matt for walking me through a proper version of VCF_BAM_utilities! Feel free to add to it, or use it to get the samples in a VCF file, a BAM file, or a collection of BAM files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5223 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-09 18:08:27 +00:00
8d0f1b75d5
Added queue/util/BAMutilities Object [with BAM and VCF parsing utilities], which is now used by my qscripts that robustly split runs by sample
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5214 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 22:17:29 +00:00
3c1a026c94
Updated script to properly bin DoC values so that down-sampling corresponds to range of DoC values obtainable
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5208 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 16:47:55 +00:00
8b8b4fced1
Removed explicit memoryLimit, so that memLimit given on the command-line will NOT be ignored...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5202 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-06 01:55:17 +00:00
4cdc974c5f
Preliminary Qscript to run DoC for the purpose of CNV detection
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5194 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 21:25:59 +00:00
7605f0e6c1
Corrected input/output definitions for Queue
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5173 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 07:39:00 +00:00
3839fd1a25
Updated phasing pipeline to properly read samples from VCF and BAM files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5172 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 07:16:05 +00:00
798955b006
After discussing with Mark, revert to "Master merging" of phase information from VCFs. This has the advantage of creating minimal phased VCFs from RBP, from which phase info is merged into the original "master VCF". Also, updated Genotype.sameGenotype() to be simpler and NOT REVERSE the ignorePhase flag in comparing Allele lists/sets
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5167 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 19:50:15 +00:00
a89400b20c
Simple implementation to retrieve relevant BAM files for each sample
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5152 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 00:03:03 +00:00
f258363cfc
Minor bug fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5150 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 22:29:28 +00:00
742bd44728
Changed output file to be user-defined
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5149 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 22:15:26 +00:00
6c99dc4dab
Take (partial) ownership of phasing 1000G chr20 calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5147 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 21:49:41 +00:00
fromer
kshakir