Changes between Version 50 and Version 51 of SnpCallingPipeline

Timestamp:

Nov 8, 2010 9:05:17 AM (14 years ago)

Author:

Morris Swertz

Comment:

--

SnpCallingPipeline

@@ -35 +35 @@
                 style=filled;
                 color=lightgrey;
+
                 "reference.fasta" -> RealignerTargetCreator -> "realign.intervals"
                 "indelcalls.vcf"-> RealignerTargetCreator 
@@ -51 +52 @@
                 "flowcell_lane.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> "IndelRealigner & \n FixMateInformation (knownsOnly)" ->"Quality Recalibration"->"flowcell_lane.aligned.bam"
                 "realign.intervals" -> "IndelRealigner & \n FixMateInformation (knownsOnly)"   
-                label = "Per Lane*Chromosome (750*3*24=54k) ";
+                label = "Per Lane (750*3=2250) ";
         }
 
@@ -69 +70 @@
 }}}
 
+Discussion
+
+* How long takes alignment per genome?
+   * If this takes very long we can split read files
+* How long takes realign knownsonly (per genome)?
+   * If very long, we need to rewrite workflow 2 to split before realign
+* For realign: if we split per chromosome, can we also split bam file?
+* How to easily lift over from b36 to b37
+  * Contact BGI if they can use b37??
+
+Todo:
+
+* Recode workflow 2 to work per genome instead of per chromosome
+
 == List of steps ==