DNAseq analysis

• 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.
• 2. Whole genome sequence data analysis
  • 2.1. WGS
    • 2.1.1. fastq QC
    • 2.1.2. Reads mapping
    • 2.1.3. Reads mapping statistics
    • 2.1.4. GATK preprocess
  • 2.2. Call Mutation
  • 2.3. Call CNV
  • 2.4. WGS SV (structural variants calling)
    • 2.4.1. call SVs from different softwares
    • 2.4.2. consensus results by jasmine
    • 2.4.3. output file type