[[TOC()]] = SNP calling pipeline = Status: Alpha Authors: Freerk van Dijk, Morris Swertz Based on [http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit Broad GATK pipeline]. To perform the analysis as fast and good as possible the pipeline has been divided into several small processes. These processes are all numbered and can be found below, including commands, input and output files starting with pre-alignment and ending with variation calling & filtering. * SnpCallingPipeline/ReferencePreparation * SnpCallingPipeline/AlignmentAndCleaning * SnpCallingPipeline/VariantCalling == Simplified Overview == This simplified overview this schema hides intermediate sort and indexing steps and only shows data inputs/outputs first time they occur. {{{#!graphviz 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" node [shape=ellipse,color=yellow] subgraph cluster_0 { 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)"; } 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)" -> "flowcell_lane.aligned.bam" "realign.intervals" -> "IndelRealigner & \n FixMateInformation (knownsOnly)" label = "Per Lane*Chromosome (750*3*24=54k) "; } 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 FixMateInformation -> IndelGenotyperV2 -> FilterSingleCalls -> UnifiedGenotyper -> Filtration -> VariantEval -> "sample QC reports" Filtration -> "sample_chr[1-24].vcf" label = "Per Sample*Chromosome (750*24=18k)"; } } }}}