Changes between Version 57 and Version 58 of SnpCallingPipeline

Timestamp:

Dec 9, 2010 9:44:13 AM (13 years ago)

Author:

Leon Mei

Comment:

--

SnpCallingPipeline

@@ -15 +15 @@
 digraph g {
 
-  size="10,10" node [shape=box,style=filled,color=white] "dbsnp" "reference.fasta" "realign.intervals" "indelcalls.vcf" "chr[1-24] .fasta" "flowcell_lane.1.fq.gz" "flowcell_lane.2.fq.gz" "flowcell_lane.aligned.bam" "flowcell_lane2.aligned.bam" "flowcell_lane3.aligned.bam" "sample.aligned.bam" "sample QC reports" "sample_chr[1-24] .vcf"
+  size="10,10" node [shape=box,style=filled,color=white] "dbsnp" "reference.fasta" "realign.intervals" "indelcalls.vcf" "chr[1-24]  .fasta" "flowcell_lane.1.fq.gz" "flowcell_lane.2.fq.gz" "flowcell_lane.aligned.bam" "flowcell_lane2.aligned.bam" "flowcell_lane3.aligned.bam" "sample.aligned.bam" "sample QC reports" "sample_chr[1-24]  .vcf"
 
   node [shape=ellipse,color=yellow]
@@ -22 +22 @@
     style=filled; color=lightgrey;
 
-  "reference.fasta" -> RealignerTargetCreator  -> "realign.intervals" "indelcalls.vcf"-> RealignerTargetCreator   "reference.fasta"->Split->"chr[1-24] .fasta"  dbsnp -> RealignerTargetCreator   label = "Per genome (1)";
+  "reference.fasta" -> RealignerTargetCreator   -> "realign.intervals" "indelcalls.vcf"-> RealignerTargetCreator    "reference.fasta"->Split->"chr[1-24]  .fasta"  dbsnp -> RealignerTargetCreator    label = "Per genome (1)";
 
 }
 
   subgraph cluster_1 {
-    style=filled; color=lightgrey; "flowcell_lane.1.fq.gz" -> align1 -> alignPE "chr[1-24] .fasta" -> align1 "chr[1-24] .fasta" -> align2 "chr[1-24] .fasta" -> alignPE "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 (750*3=2250) ";
+    style=filled; color=lightgrey; "flowcell_lane.1.fq.gz" -> align1 -> alignPE "chr[1-24]  .fasta" -> align1 "chr[1-24]  .fasta" -> align2 "chr[1-24]  .fasta" -> alignPE "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 (750*3=2250) ";
   }
 
   subgraph cluster_2 {
-    style=filled; color=lightgrey; "flowcell_lane.aligned.bam" -> Merge -> "sample.aligned.bam" -> "IndelRealigner  & FixMateInformation " "flowcell_lane2.aligned.bam" -> Merge "flowcell_lane3.aligned.bam" -> Merge "IndelRealigner  & FixMateInformation " -> IndelGenotyperV2 -> FilterSingleCalls  -> UnifiedGenotyper  -> Filtration -> VariantEval  -> "sample QC reports"
+    style=filled; color=lightgrey; "flowcell_lane.aligned.bam" -> Merge -> "sample.aligned.bam" -> "IndelRealigner   & FixMateInformation  " "flowcell_lane2.aligned.bam" -> Merge "flowcell_lane3.aligned.bam" -> Merge "IndelRealigner   & FixMateInformation  " -> IndelGenotyperV2 -> FilterSingleCalls   -> UnifiedGenotyper   -> Filtration -> VariantEval   -> "sample QC reports"
 
 Filtration -> "sample_chr[1-24].vcf"
@@ -42 +42 @@
     style=filled; color=lightgrey;
 
-  "sample.aligned.bam" -> "UnifiedGenotype  (without realign)"->"QC against arrays and BGI"
+  "sample.aligned.bam" -> "UnifiedGenotype   (without realign)"->"QC against arrays and BGI"
 
   label = "QC per sample";
@@ -86 +86 @@
 ==  ==
 == Optimization? ==
-{{{
-{| {{table}}
-| align="center" style="background:#f0f0f0;"|'''Step'''
-| align="center" style="background:#f0f0f0;"|'''Cores'''
-| align="center" style="background:#f0f0f0;"|'''Memory (gb)'''
-| align="center" style="background:#f0f0f0;"|'''Time (hh.mm)'''
-|-
-| BWA alignment||1||± 6||10.05
-|-
-| BWA spe||1||||3.35
-|-
-| Sam-Bam||1||||12.3
-|-
-| Sam sort||1||||5.05
-|-
-| Mark Duplicates||1||4||1.55
-|-
-| Realignment (knowns only)||1||8 (*can be lowered)||5.2
-|-
-| Fix mates||1||6 (*)||3.05
-|-
-| Covariates bef.||1||2||12.35
-|-
-| Recalibrate||1||4||7.3
-|-
-| Sam sort||1||||4.5
-|-
-| Covariates aft.||1||2||11.2
-|-
-| Analyze Covar.||1||4||< 00.01
-|-
-| Total||||||± 90 (< 4 days)
-|-
-| 
-|}
-}}}
-=== Disk ===
+==== Current ====
+Step    Cores    Memory (gb)    Time (hh.mm)[[BR]]BWA alignment    1    ± 6    10.05[[BR]]BWA spe    1        3.35[[BR]]Sam-Bam    1        12.3[[BR]]Sam sort    1        5.05[[BR]]Mark Duplicates    1    4    1.55[[BR]]Realignment (knowns only)    1    8 (*can be lowered)    5.2[[BR]]Fix mates    1    6 (*)    3.05[[BR]]Covariates bef.    1    2    12.35[[BR]]Recalibrate    1    4    7.3[[BR]]Sam sort    1        4.5[[BR]]Covariates aft.    1    2    11.2[[BR]]Analyze Covar.    1    4    < 00.01
+
+==== Disk ====
  * Option 1, If it is possible to let a node guarantee certain amount of disk space (/tmp), we should use the entire cluster. Before start running a pipeline, we can just ask the node to reserve that amount of disk space.
  * Option 2, If we can cut a dedicate part of the cluster, we can use our own scheduler to share the nodes/disks. E.g, depending on the disk space usage pattern and how we can remove the data, we can decide which jobs run at which node and when.
 
-=== Memory/CPU time ===
- * Can multiple samples use the same reference genome in memory during the BWA alignment. I.e. 1 sample->6GB, 3 samples->6GB. 
+==== Memory/CPU time ====
+ * Can multiple samples use the same reference genome in memory during the BWA alignment. I.e. 1 sample->6GB, 3 samples->6GB.
    * NO?
- * Can we parallelize the Markduplicate? 
+ * Can we parallelize the Markduplicate?
    * YES!
    * !MarkDuplicates finds sequence pairs that map to the same position, marking or removing the duplicates so you can work with unique pairs in downstream analyses. If you want them removed, use the REMOVE_DUPLICATES=true flag when running the program.
- * Can we parallelize covariate before/after, recalibration? 
+ * Can we parallelize covariate before/after, recalibration?
    * Don't know