Overview

Short pipeline that forks umi-processing call structural variance of targeted sequencing data. It calls delly for calling and genotyping.

Input:

• mapped BAM files (umi-processing until the fastqc step)
• reference genome

Output:

• filtered: somatic SVC
• merged: genotyped SVC

Workflow

• A: SV calling on the BAM files of samples
• A: merge all SV calls into unified site list
• A: use merged calls list to genotype samples
• A: merge all genotyped samples
• ############ Skipped! ##########
• A: use merged genotype list for germline filtering
• ############ end Skipped! ######
• B: SV calling on the BAM files of control
• B: merge all control SV calls into unified site list
• C: "setDIFF" sample SV calls with contol SV calls