fromer
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0b45de14ed
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Some minor updates to fully utilize the functionality of reduceByInterval
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5411 348d0f76-0448-11de-a6fe-93d51630548a
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2011-03-09 20:38:08 +00:00 |
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fromer
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d6e3f2eba6
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Added GC content calculator for CNV data
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5240 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-14 22:29:55 +00:00 |
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fromer
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cdf53188d6
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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!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5231 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-11 19:14:42 +00:00 |
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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 |
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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 |
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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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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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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 |