User contributions
From Genome Analysis Wiki
Jump to navigationJump to search- 12:35, 11 July 2014 diff hist -6 SeqShop: Analysis of Structural Variation Practical, June 2014 →Running GotCloud/GenomeSTRiP Metadata Pipeline
- 12:31, 11 July 2014 diff hist -72 SeqShop: Analysis of Structural Variation Practical, June 2014 →Why do we use GotCloud/GenomeSTRiP pipeline instead of directly using GenomeSTRiP itself?
- 12:42, 10 July 2014 diff hist +89 EPACTS
- 12:41, 10 July 2014 diff hist +79 EPACTS
- 12:40, 10 July 2014 diff hist +79 EPACTS →Lastest ChangeLog
- 16:00, 19 June 2014 diff hist -1 SeqShop: Genetic Association Analysis Practical, June 2014 →Setup your run environment
- 15:31, 19 June 2014 diff hist +9 SeqShop: Genetic Association Analysis Practical, June 2014
- 12:51, 19 June 2014 diff hist 0 SeqShop: Genetic Association Analysis Practical, June 2014 →Goals of This Session
- 12:51, 19 June 2014 diff hist +2 SeqShop: Genetic Association Analysis Practical, June 2014 →Goals of This Session
- 12:51, 19 June 2014 diff hist +117 SeqShop: Genetic Association Analysis Practical, June 2014
- 12:50, 19 June 2014 diff hist 0 N File:Seqshop association practice 2014 06.pdf current
- 12:50, 19 June 2014 diff hist 0 File:Seqshop association 2014 06.pdf Hmkang uploaded a new version of "File:Seqshop association 2014 06.pdf" current
- 12:47, 19 June 2014 diff hist 0 N File:Seqshop association 2014 06.pdf
- 12:45, 19 June 2014 diff hist -300 SeqShop: Genetic Association Analysis Practical, June 2014 →Phenotype Information
- 12:44, 19 June 2014 diff hist +43 SeqShop: Genetic Association Analysis Practical, June 2014 →Setup your run environment
- 12:43, 19 June 2014 diff hist +3,991 SeqShop: Genetic Association Analysis Practical, June 2014
- 12:34, 19 June 2014 diff hist 0 N File:Single.zoom.22.36995620.png current
- 12:33, 19 June 2014 diff hist 0 N File:Single.epacts.mh.png current
- 12:33, 19 June 2014 diff hist 0 N File:Single.epacts.qq.png
- 12:33, 19 June 2014 diff hist 0 N File:Emmax.epacts.qq.pdf current
- 12:23, 19 June 2014 diff hist +433 SeqShop: Genetic Association Analysis Practical, June 2014
- 02:51, 19 June 2014 diff hist +536 SeqShop: Genetic Association Analysis Practical, June 2014 →Annotating Variants with EPACTS
- 02:18, 19 June 2014 diff hist +1,777 SeqShop: Genetic Association Analysis Practical, June 2014 →Annotating Variants with EPACTS
- 02:08, 19 June 2014 diff hist +10,800 N SeqShop: Genetic Association Analysis Practical, June 2014 Created page with "(''WARNING: Under Construction'') == Goals of This Session == * Understand how to annotate variants using EPACTS * Understand how to run single variant association analysis u..."
- 00:02, 19 June 2014 diff hist 0 EPACTS
- 01:43, 18 June 2014 diff hist 0 File:Seqshop cnv partb 2014 06.pdf Hmkang uploaded a new version of "File:Seqshop cnv partb 2014 06.pdf" current
- 01:39, 18 June 2014 diff hist 0 File:Seqshop cnv partb 2014 06.pdf Hmkang uploaded a new version of "File:Seqshop cnv partb 2014 06.pdf"
- 01:37, 18 June 2014 diff hist +1 SeqShop: Analysis of Structural Variation Practical, June 2014 →Goals of This Session
- 01:37, 18 June 2014 diff hist -2 SeqShop: Analysis of Structural Variation Practical, June 2014 →Goals of This Session
- 01:36, 18 June 2014 diff hist +102 SeqShop: Analysis of Structural Variation Practical, June 2014 →Goals of This Session
- 01:35, 18 June 2014 diff hist 0 N File:Seqshop cnv partb 2014 06.pdf
- 01:29, 18 June 2014 diff hist -35 SeqShop: Analysis of Structural Variation Practical, June 2014
- 01:28, 18 June 2014 diff hist -2 SeqShop: Analysis of Structural Variation Practical, June 2014 →Running GotCloud/GenomeSTRiP 3rd-party Site Genotyping/Filtering Pipeline
- 01:22, 18 June 2014 diff hist +1 SeqShop: Analysis of Structural Variation Practical, June 2014 →Running GotCloud/GenomeSTRiP Metadata Pipeline
- 01:22, 18 June 2014 diff hist +10 SeqShop: Analysis of Structural Variation Practical, June 2014 →Running GotCloud/GenomeSTRiP Metadata Pipeline
- 01:20, 18 June 2014 diff hist +134 SeqShop: Analysis of Structural Variation Practical, June 2014 →Why use GenomeSTRiP?
- 01:18, 18 June 2014 diff hist 0 SeqShop: Analysis of Structural Variation Practical, June 2014 →Why do we use GotCloud/GenomeSTRiP pipeline instead of directly using GenomeSTRiP itself?
- 01:17, 18 June 2014 diff hist -7 SeqShop: Analysis of Structural Variation Practical, June 2014 →Sequnce Alignment Files: BAM Files and Index Files
- 01:17, 18 June 2014 diff hist +48 SeqShop: Analysis of Structural Variation Practical, June 2014 →Sequnce Alignment Files: BAM Files and Index Files
- 01:15, 18 June 2014 diff hist +147 SeqShop: Analysis of Structural Variation Practical, June 2014 →Running GotCloud/GenomeSTRiP Discovery Pipeline
- 01:13, 18 June 2014 diff hist +1 SeqShop: Analysis of Structural Variation Practical, June 2014
- 01:12, 18 June 2014 diff hist -8,894 SeqShop: Analysis of Structural Variation Practical, June 2014
- 01:12, 18 June 2014 diff hist +1 SeqShop: Analysis of Structural Variation Practical, June 2014 →What does a real SV look like?
- 01:11, 18 June 2014 diff hist +1,988 SeqShop: Analysis of Structural Variation Practical, June 2014 →Running GotCloud/GenomeSTRiP Discovery Pipeline
- 01:08, 18 June 2014 diff hist 0 N File:Genomestrip thirdparty screenshot.png current
- 00:58, 18 June 2014 diff hist 0 N File:Genomestrip genotype screenshot.png current
- 00:55, 18 June 2014 diff hist 0 N File:Igvsvexample.png current
- 00:14, 18 June 2014 diff hist +699 SeqShop: Analysis of Structural Variation Practical, June 2014 →How many variants are filtered out?
- 00:13, 18 June 2014 diff hist 0 N File:Genomestrip filter description.png current
- 00:07, 18 June 2014 diff hist 0 SeqShop: Analysis of Structural Variation Practical, June 2014 →How many variants are filtered out?
- 00:07, 18 June 2014 diff hist 0 SeqShop: Analysis of Structural Variation Practical, June 2014 →How many variants are filtered out?
- 00:06, 18 June 2014 diff hist +132 SeqShop: Analysis of Structural Variation Practical, June 2014 →How many variants are filtered out?
- 00:05, 18 June 2014 diff hist +713 SeqShop: Analysis of Structural Variation Practical, June 2014 →Running GotCloud/GenomeSTRiP Discovery Pipeline
- 00:03, 18 June 2014 diff hist -1 SeqShop: Analysis of Structural Variation Practical, June 2014 →Overview of GotCloud/GenomeSTRiP pipeline
- 00:02, 18 June 2014 diff hist +346 SeqShop: Analysis of Structural Variation Practical, June 2014 →Setup your run environment
- 23:56, 17 June 2014 diff hist +53 SeqShop: Analysis of Structural Variation Practical, June 2014 →Running GotCloud/GenomeSTRiP Discovery Pipeline
- 23:55, 17 June 2014 diff hist 0 N File:Genomestrip discovery screenshot.png current
- 23:53, 17 June 2014 diff hist +26 SeqShop: Analysis of Structural Variation Practical, June 2014 →Setup your run environment
- 23:52, 17 June 2014 diff hist +3,323 SeqShop: Analysis of Structural Variation Practical, June 2014 →Run GotCloud/GenomeSTRiP pipeline
- 23:14, 17 June 2014 diff hist -6 SeqShop: Analysis of Structural Variation Practical, June 2014 →Run GotCloud/GenomeSTRiP pipeline
- 15:10, 17 June 2014 diff hist +833 SeqShop: Analysis of Structural Variation Practical, June 2014
- 14:56, 17 June 2014 diff hist -185 SeqShop: Analysis of Structural Variation Practical, June 2014 →Reference Files
- 14:56, 17 June 2014 diff hist +990 SeqShop: Analysis of Structural Variation Practical, June 2014
- 14:47, 17 June 2014 diff hist +21 SeqShop: Analysis of Structural Variation Practical, June 2014 →Reference Files
- 14:46, 17 June 2014 diff hist +971 SeqShop: Analysis of Structural Variation Practical, June 2014
- 09:46, 17 June 2014 diff hist -54 SeqShop: Analysis of Structural Variation Practical, June 2014
- 09:43, 17 June 2014 diff hist -3 SeqShop: Analysis of Structural Variation Practical, June 2014 →Genotype Refinement Output
- 09:39, 17 June 2014 diff hist +1 SeqShop: Variant Calling and Filtering for INDELs Practical, June 2014 →Header
- 09:37, 17 June 2014 diff hist 0 N File:Gotcloudmemotyexome.png current
- 09:36, 17 June 2014 diff hist 0 N File:Gotcloudruntimewgs.png current
- 09:22, 17 June 2014 diff hist +167 SeqShop: Variant Calling and Filtering for SNPs Practical, June 2014 →Run GotCloud SnpCall
- 09:19, 17 June 2014 diff hist 0 N File:Gotcloudoverview.png current
- 02:31, 17 June 2014 diff hist -1 SeqShop: Variant Calling and Filtering for INDELs Practical, June 2014 →Did I find interesting variants?
- 02:29, 17 June 2014 diff hist +32 SeqShop: Variant Calling and Filtering for INDELs Practical, June 2014 →Examining GotCloud indel Ouptut
- 02:28, 17 June 2014 diff hist +521 SeqShop: Variant Calling and Filtering for INDELs Practical, June 2014 →Did I find interesting variants?
- 02:27, 17 June 2014 diff hist 0 N File:Samtoolsviewindel.png current
- 02:22, 17 June 2014 diff hist +135 SeqShop: Variant Calling and Filtering for SNPs Practical, June 2014 →Did I find interesting variants?
- 02:21, 17 June 2014 diff hist +915 SeqShop: Variant Calling and Filtering for SNPs Practical, June 2014 →Did I find interesting variants?
- 02:20, 17 June 2014 diff hist 0 N File:Samtoolstviewsnp.png current
- 01:42, 17 June 2014 diff hist +35 SeqShop: Analysis of Structural Variation Practical, June 2014
- 01:41, 17 June 2014 diff hist +13,984 N SeqShop: Analysis of Structural Variation Practical, June 2014 Created page with "==Introduction== See the introductory slides for an intro to this tutorial. == Goals of This Session == * What we want to learn is ca..."
- 01:14, 17 June 2014 diff hist -528 SeqShop: Variant Calling and Filtering for INDELs Practical, June 2014 →Records
- 01:02, 17 June 2014 diff hist 0 SeqShop: Variant Calling and Filtering for INDELs Practical, June 2014 →Did I find interesting variants?
- 01:01, 17 June 2014 diff hist +2 SeqShop: Variant Calling and Filtering for INDELs Practical, June 2014 →Did I find interesting variants?
- 01:01, 17 June 2014 diff hist +1,874 SeqShop: Variant Calling and Filtering for INDELs Practical, June 2014 →Examining GotCloud indel Ouptut
- 00:50, 17 June 2014 diff hist 0 File:EvsAPOL1b.png Hmkang uploaded a new version of "File:EvsAPOL1b.png" current
- 00:43, 17 June 2014 diff hist +15 SeqShop: Variant Calling and Filtering for SNPs Practical, June 2014 →Did I find interesting variants?
- 00:40, 17 June 2014 diff hist 0 N File:EvsAPOL1b.png
- 00:40, 17 June 2014 diff hist 0 N File:EvsAPOL1a.png current
- 00:14, 17 June 2014 diff hist +529 SeqShop: Variant Calling and Filtering for SNPs Practical, June 2014 →Genotype Refinement Output
- 23:43, 16 June 2014 diff hist +75 SeqShop: Sequence Mapping and Assembly Practical, June 2014 →Reference Files
- 23:42, 16 June 2014 diff hist +172 SeqShop: Sequence Mapping and Assembly Practical, June 2014 →Reference Files
- 23:39, 16 June 2014 diff hist +258 SeqShop: Sequence Mapping and Assembly Practical, June 2014 →Run GotCloud Align
- 23:36, 16 June 2014 diff hist 0 N File:Gotcloud align detail.png current
- 23:31, 16 June 2014 diff hist +9 SeqShop: Variant Calling and Filtering for SNPs Practical, June 2014 →Filtering Summary Statistics
- 23:31, 16 June 2014 diff hist +116 SeqShop: Variant Calling and Filtering for SNPs Practical, June 2014 →Filtering Summary Statistics
- 23:30, 16 June 2014 diff hist +7 Understanding vcf-summary output →Rows of vcf-summary output has three sections
- 23:29, 16 June 2014 diff hist -1 Understanding vcf-summary output →What should we expect from good SNP call sets?
- 23:29, 16 June 2014 diff hist +3,751 Understanding vcf-summary output
- 22:46, 16 June 2014 diff hist +1,284 N Understanding vcf-summary output Created page with "== What is vcf-summary? == <code>vcf-summary</code> is a utility included in GotCloud that helps evaluate the quality of SNP calls. Because GotCloud will automaticall..."