carneiro
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c630701a76
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Following Ryan's suggestion, I am moving the Methods Development Calling pipeline to the Core.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5226 348d0f76-0448-11de-a6fe-93d51630548a
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2011-02-10 17:36:05 +00:00 |
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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 |
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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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 |
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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 |
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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 |
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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 |
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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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 |