Read Mapping and SAM BAM - iffatAGheyas/bioinformatics-tutorial-wiki GitHub Wiki

Read Mapping & SAM/BAM

• Overview
  What is read mapping and why we use SAM/BAM formats

• Reference Genome Preparation

  • Downloading or building a FASTA reference
  • Indexing with BWA/Bowtie2/minimap2

• Aligning Reads

  • BWA-MEM
  • Bowtie2
  • Minimap2

• SAM Format Deep Dive

  • Mandatory fields (QNAME, FLAG, RNAME, etc.)
  • SAM FLAG bits explained
  • CIGAR strings (matches, insertions, deletions)
  • Optional tags

• BAM Processing with samtools

  • Converting SAM → BAM (samtools view)
  • Sorting (samtools sort)
  • Indexing (samtools index)
  • Quick statistics (samtools flagstat, samtools idxstats)

• Coverage & Depth Analysis

  • samtools depth
  • bedtools genomecov

• Filtering & Cleanup

  • Removing PCR duplicates
  • Filtering by mapping quality / FLAG

• Alignment Visualization

  • Loading BAM in IGV or Tablet

• Hands-On Exercise

  1. Map simulated (or real) reads
  2. Generate & index BAM
  3. Evaluate mapping rates, coverage and QC metrics