Variation Analysis

Package Overview

Goal

Identification of sequence variants in germline and somatic samples, in whole-genomes and exomes

Requirements

• Paired-end sequencing with 100bp read length or more
• Germline:
  • 40x technical coverage (read length*2 / length of genome or exome)
  • Unique molecular identifiers (UMIs) or amplification-free library preparation suggested
• Somatic:
  • Paired germline controls highly recommended
  • UMIs or amplification-free library preparation highly recommended
  • Unique-dual indexing of samples
  • 100x technical coverage for somatic samples for exome
  • 40x technical coverage for germline controls for exome
  • 60x technical coverage for somatic samples for whole-genome
  • 40x technical coverage for germline controls for whole-genome

Analysis

• Running the nf-core sarek pipeline
  • Trimming of adapters and low-quality bases, processing of UMIs
  • Mapping to a reference
  • Identification and genotyping of SNVs and small indels
  • Functional annotation of variants based on a defined set of databases

Output

• Mapped reads for visual inspection
• Variant tables with genotype information (germline only) and annotation
• HTML report

Advanced Analysis

• Analysis of large sample sets (exomes: >= 100 samples, genomes: >= 20 samples)
• Identification of copy-number variants including functional annotation
• Identification of structural variants including functional annotation