domains / families / science / alignment-sorting

alignment-sorting

separate

Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.

When to use

• Sort alignment files by coordinate
• Sort alignment files by read name
• Prepare BAM files for indexing
• Prepare BAM files for variant calling
• Prepare BAM files for paired-end analysis
• Check sort order of BAM files
• Combine multiple BAM files

When not to use

• In-Python sorting of BAM records

Skill page

Source