README.md

Calling Structural Variations

This is an HPC pipeline for calling structural variations using three software from 76 matched tumor-normal whole genome sequencing (WGS) bams from 38 childhood acute lymphoblastic leukemia cases.

Smoove (lumpy)

• 1.1.PreMergeSVPerSampleSmoove.sh
• 1.2.SmooveUnionSites.sh
• 1.3.SmooveGenotype.sh
• 1.4.SmoovePasteAnnotate.sh

Manta

• 2.1.PreMergeSVPerSampleMantaconfigure.sh
• 2.2.MantaWorkflow.sh
• 2.3.MantaClean.sh

Delly

• 3.1.DellyPerSampleCall.sh
• 3.2.DellyPrefilter.sh
• 3.3.DellyGeno.sh
• 3.4.DellyPostfilter.sh
• 3.5.DellyBcf2vcf.sh

Finding variants that were called by at least 2 callers

• 4.1.Survivor.sh

Annotate variants

• 4.2.Anno.sh

Create Venn diagram, histograms and html files

• 4.3.Summary.sh

an example Venn graph: