NGS: Picard

Conversion

• 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