SNP calling pipeline

Status: Alpha Authors: Freerk van Dijk, Morris Swertz

This is the documentation of the BBMRI-NL snp calling pipeline based on the ​Broad GATK. It consists of the following three workflows:

• Workflow 1: SnpCallingPipeline/ReferencePreparation
• Workflow 2: SnpCallingPipeline/AlignmentAndCleaning
• Workflow 3: 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.

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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:

First:

• Recode workflow 2 to work per genome instead of per chromosome and test - Freerk (done) -> workflow3 still needs to be done
• Run on pilot data (6) to evaluate timing and concurrency issues (can 6 run on one node?) - Freerk (in progress)
• Complete analysis of data (60) until including merge to sample.aligned.bam - Freerk
• QC pipeline - Can we get Jeroen and Yurii involved here
  • UnifiedGenotyper? without realign - Freerk
  • GATK variant eval to make venn diagrams
  • Contact Yurii for this; Let Jeroen take charge? (done) -> Jeroen doing QC stuff
• Share data with Grid following plan Silvia - Freerk
• Contact BGI for sample list - Morris (done)
• Put report on FTP - Ger,Freerk

Next:

• Short tutorial howto generate pipeline scripts - Morris
  • Teach Barbara and Jeroen
• Port pipeline to Grid with help of Barbara
  • What do we need to generate exactly - Barbara

List of steps

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