Ancient DNA session

Welcome to the Ancient DNA session of the advanced course “Archaeogenetics approaches to investigate domestication and evolution”, CIBIO, Porto (20-24 May 2019), by Claudio Ottoni (Sapienza University of Rome).

Contents

• 1. List of Tools
• 2. Quality filtering of reads
  • 2.1. Reads quality control
  • 2.2. Reads quality filtering
• 3. Preparation of the reference sequence
  • 3.1. Index the reference sequence with BWA
  • 3.2. Create a reference dictionary
  • 3.3. Index the reference sequence with Samtools
• 4. Alignment of the reads to the reference sequence
  • 4.1. Alignment of pre-processed reads to the reference genome with BWA aln
  • 4.2. Converting sam file to bam file
  • 4.3. Sorting and indexing the bam file
  • 4.4. Adding Read Group tags and indexing bam files
  • 4.5. Marking and removing duplicates
  • 4.6. Local realignment of reads
  • 4.7. Generate flagstat file
  • 4.8. Visualization of reads alignment
• 5. Create Summary Reports
• 6. Damage analysis and quality rescaling of the BAM file
• 7. Variant calling and visualization
  • 7.1. Variants calling
  • 7.2. Variants visualization

• Index
• Module Index
• Search Page