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 |
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 |
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 |
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 |
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 |