fromer
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947cc44854
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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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5223 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-09 18:08:27 +00:00 |
kshakir
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4d1cca95bb
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Removed deprecated getDbsnpFile.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5221 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-08 21:12:15 +00:00 |
carneiro
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e5cfc6ae74
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NA12878 hg19 dataset was included to the methods pipeline. (and I am running it)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5217 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-08 16:17:46 +00:00 |
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fromer
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8d0f1b75d5
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Added queue/util/BAMutilities Object [with BAM and VCF parsing utilities], which is now used by my qscripts that robustly split runs by sample
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5214 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-07 22:17:29 +00:00 |
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fromer
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3c1a026c94
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Updated script to properly bin DoC values so that down-sampling corresponds to range of DoC values obtainable
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5208 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-07 16:47:55 +00:00 |
depristo
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c4707631e2
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MethodsDevelopmentPipeline is now the test bed for large scale AWS_S3 logging. Can be disabled from command line if this is necessary
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5203 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-06 17:03:45 +00:00 |
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fromer
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8b8b4fced1
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Removed explicit memoryLimit, so that memLimit given on the command-line will NOT be ignored...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5202 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-06 01:55:17 +00:00 |
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depristo
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fe4aa58d35
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Removing unused class
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5197 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-04 22:22:28 +00:00 |
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fromer
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4cdc974c5f
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Preliminary Qscript to run DoC for the purpose of CNV detection
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5194 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-04 21:25:59 +00:00 |
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carneiro
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358a400474
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made ApplyVariantCut a default part of the pipeline, added the -noCut option if you don't want to use it.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5189 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-03 19:29:36 +00:00 |
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carneiro
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7af003666d
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added optional argument -cut to apply the variant cut to the ts recalibrated vcf.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5183 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-03 17:34:40 +00:00 |
chartl
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5398cf620a
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Bug fixes in the in process function (spoiled by python: was not closing my writers). SortByRef now works somewhat like the perl script does, rather than doing a memory-expensive sort. Adding a QTools qscript which is kinda clunky, and will be used mostly for integration tests of these IPFs, pending some better way to construct argument collections and function accessors at compile-time.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5182 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-03 17:32:46 +00:00 |
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carneiro
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cf15819db5
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updated to work with the new VariantEval.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5176 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-02 17:46:07 +00:00 |
rpoplin
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47357b726e
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Fixing import GenotypeCalculationModel since it doesn't exist anymore.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5175 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-02 15:39:43 +00:00 |
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fromer
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7605f0e6c1
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Corrected input/output definitions for Queue
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5173 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-02 07:39:00 +00:00 |
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fromer
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3839fd1a25
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Updated phasing pipeline to properly read samples from VCF and BAM files
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5172 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-02 07:16:05 +00:00 |
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fromer
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798955b006
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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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5167 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-01 19:50:15 +00:00 |
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fromer
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a89400b20c
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Simple implementation to retrieve relevant BAM files for each sample
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5152 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-01 00:03:03 +00:00 |
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fromer
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f258363cfc
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Minor bug fix
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5150 348d0f76-0448-11de-a6fe-93d51630548a
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2011-01-31 22:29:28 +00:00 |
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fromer
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742bd44728
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Changed output file to be user-defined
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5149 348d0f76-0448-11de-a6fe-93d51630548a
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2011-01-31 22:15:26 +00:00 |
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fromer
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6c99dc4dab
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Take (partial) ownership of phasing 1000G chr20 calls
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5147 348d0f76-0448-11de-a6fe-93d51630548a
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2011-01-31 21:49:41 +00:00 |
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carneiro
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cae4b9b0de
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quick update with the correct CEU trio bam file and it's final location.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5098 348d0f76-0448-11de-a6fe-93d51630548a
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2011-01-27 19:17:19 +00:00 |
ebanks
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68729045ca
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Always best to use the left-aligned version of the dbsnp vcf
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5091 348d0f76-0448-11de-a6fe-93d51630548a
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2011-01-26 20:21:50 +00:00 |
delangel
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fa0c476b82
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Script for calling indels in all phase 1 samples - VQSR part still needs work but raw calling is done
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5052 348d0f76-0448-11de-a6fe-93d51630548a
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2011-01-22 14:07:10 +00:00 |
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carneiro
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a0731eaa81
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updated NA12878 Trio gold standard data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5048 348d0f76-0448-11de-a6fe-93d51630548a
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2011-01-21 18:48:31 +00:00 |
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depristo
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94b64ec54a
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Moving scala script into analysis directory
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5047 348d0f76-0448-11de-a6fe-93d51630548a
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2011-01-21 18:42:18 +00:00 |
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depristo
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b45566760e
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intermediate checkin
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5045 348d0f76-0448-11de-a6fe-93d51630548a
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2011-01-21 18:39:25 +00:00 |
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rpoplin
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b6497c404f
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Moving Phase1Calling qscript over to using the cleaned, pre-BAQed bams
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5039 348d0f76-0448-11de-a6fe-93d51630548a
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2011-01-21 02:41:20 +00:00 |
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carneiro
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fc73569d62
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Added NA12878 Trio dataset to the pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5037 348d0f76-0448-11de-a6fe-93d51630548a
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2011-01-20 23:15:33 +00:00 |
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depristo
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41c8552d0a
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Added implements HasGenomeLocation to all revelant classes. It's not possible to write generic code for working with objects that support the getLocation() function in HasGenomeLocation. Please, if you have an object that has a location, implement this interface and start using / writing generic functions to sort, compare, etc. these objects.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5031 348d0f76-0448-11de-a6fe-93d51630548a
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2011-01-20 12:54:03 +00:00 |
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rpoplin
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55eb0387ac
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Another relevant qscript. I use this one to do thousands of variant recalibration jobs to search for optimal parameters.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5019 348d0f76-0448-11de-a6fe-93d51630548a
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2011-01-19 18:17:32 +00:00 |
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chartl
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a463dbcda1
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Refactoring the qscript directory; oneoffs, playground, and core
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5017 348d0f76-0448-11de-a6fe-93d51630548a
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2011-01-19 15:23:40 +00:00 |