Changes between Version 54 and Version 55 of SnpCallingPipeline

Timestamp:

Nov 8, 2010 9:36:48 AM (14 years ago)

Author:

Morris Swertz

Comment:

--

SnpCallingPipeline

@@ -70 +70 @@
                 color=lightgrey;
 
-                "sample.aligned.bam" -> "TODO compare against arrays and BGI output"
+                "sample.aligned.bam" -> "UnifiedGenotype (without realign)"->"QC against arrays and BGI"
 
                 label = "QC per sample";
@@ -92 +92 @@
 Todo:
 
-* Recode workflow 2 to work per genome instead of per chromosome
-* QC pipeline
-   * Simple SNP caller
+First:
+* Recode workflow 2 to work per genome instead of per chromosome and test - Freerk
+* Run on pilot data (6) to evaluate timing and concurrency issues (can 6 run on one node?) - Freerk
+* Complete analysis of data (60) until including merge to sample.aligned.bam - Freerk
+* QC pipeline - Can we get Jeroen and Yurii involved here
+   * UnifiedGenotyper without realign - Freerk
    * GATK variant eval to make venn diagrams
-   * Contact Yurii for this; Let Jeroen take charge?
+   * Contact Yurii for this; Let Jeroen take charge? 
+* Share data with Grid following plan Silvia - Freerk
+* Contact BGI for sample list - Morris
+* Put report on FTP - Ger,Freerk
 
+Next:
+* Short tutorial howto generate pipeline scripts - Morris
+   * Teach Barbara and Jeroen
+* Port pipeline to Grid with help of Barbara
+   * What do we need to generate exactly - Barbara 
 == List of steps ==