SNP calling pipeline

Status: Alpha

Authors: Freerk van Dijk, Morris Swertz

Based on ​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

Schematic Overview

This simplified overview this schema hides intermediate sort and indexing steps and only shows data inputs/outputs first time they occur.

Error: Failed to load processor graphviz

No macro or processor named 'graphviz' found

List of steps

Table of Contents

1. Workflow 1: genome reference file creation
   1. clean-fasta-headers
   2. split-vcf-chr for dbsnp and indels
   3. index-chromosomes
   4. bwa-index-chromosomes
   5. RealignerTargetCreator
2. Workflow 2: Alignment per Lane, per Chr
   1. bwa-align-pe
   2. bwa-align-pe
   3. sam-to-bam
   4. sam-sort
   5. gatk-MarkDuplicates
   6. gatk-IndelRealigner-KnownsOnly
   7. gatk-FixMateInformation
   8. gatk-CountCovariates
   9. gatk-TableRecalibration
   10. Repeat: sam-sort, sam-index, countcovariates
3. Workflow 3: sample level variant calling
   1. merge-lanes
   2. RealignerTargetCreator
   3. IndelRealigner
   4. FixMateInformation
   5. IndelGenotyperV2
   6. filterSingleSampleCalls
   7. UnifiedGenotyper
   8. makeIndelMask
   9. VariantFiltration
   10. MergeVcfs
   11. ChipVcf
   12. VariantEval
   13. Dindel