1. Whole exome sequence data analysis

• 1.1. WES
  • 1.1.1. QC
    • 1.1.1.1. fastp
    • 1.1.1.2. Conpair
  • 1.1.2. Reads mapping and PCR deduplication
  • 1.1.3. Reads mapping statistics
  • 1.1.4. GATK preprocess
  • 1.1.5. copy-number-variants
• 1.2. Call Mutation
  • 1.2.1. Call Mutation from Different sortwares
    • 1.2.1.1. GATK HaploCallers
    • 1.2.1.2. Mutect2
    • 1.2.1.3. Muse
    • 1.2.1.4. CaveMan
  • 1.2.2. Annotation variants
  • 1.2.3. consensus result from multiple callers
  • 1.2.4. Output file types
• 1.3. Call CNV
  • 1.3.1. Control-FREEC
• 1.4. WES
  • 1.4.1.