NGS: PicardΒΆ


  • FASTQ to BAM creates an unaligned BAM file
  • SAM to FASTQ creates a FASTQ file

QC/Metrics for SAM/BAM

  • BAM Index Statistics
  • SAM/BAM Alignment Summary Metrics
  • SAM/BAM GC Bias Metrics
  • Estimate Library Complexity
  • Insertion size metrics for PAIRED data
  • SAM/BAM Hybrid Selection Metrics for targeted resequencing data

BAM/SAM Cleaning

  • Add or Replace Groups
  • Reorder SAM/BAM
  • Replace SAM/BAM Header
  • Paired Read Mate Fixer for paired data
  • Mark Duplicate reads