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bio-alignment-sorting

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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
• Sort alignment files by tag
• Collate paired reads
• Check sort order
• Merge multiple BAM files
• Align and sort workflow
• Re-sort for duplicate marking

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