Changes between Version 19 and Version 20 of SnpCallingPipeline

Timestamp:

Oct 16, 2010 5:53:51 PM (14 years ago)

Author:

Morris Swertz

Comment:

--

SnpCallingPipeline

@@ -23 +23 @@
                 "reference.fasta" -> RealignerTargetCreator -> "realign.intervals"
                 "indelcalls.vcf"-> RealignerTargetCreator 
+                "reference.fasta"->Split->"chr[1-24].fasta" 
                 dbsnp -> RealignerTargetCreator 
                 label = "Per genome";
@@ -32 +33 @@
                 node [style=filled,color=white];
                 "Reads.1fq.gz" -> align1 -> alignPE
-                "reference.fasta"->Split->"chrN.fasta" -> align1
-                "chrN.fasta" -> align2
-                "chrN.fasta" -> alignPE
+                "chr[1-24].fasta" -> align1
+                "chr[1-24].fasta" -> align2
+                "chr[1-24].fasta" -> alignPE
                 "Reads.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> RealignIndelsAndFixMates -> "Lane.aligned.bam"
                 "realign.intervals" -> RealignIndelsAndFixMates   
-                label = "Per lane";
+                label = "Per lane/Per chromosome";
         }
 
@@ -49 +50 @@
                 RealignIndelsAndFixMates2 -> IndelGenotyperV2 -> FilterSingleCalls -> UnifiedGenotyper -> Filtration -> VariantEval -> "QC reports"
 Filtration -> VCF
-                label = "Per Sample";
+                label = "Per Sample/Per Chromosome";
         }