npm

sambamba

Fast tools for processing SAM/BAM alignment files

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About

Tools for working with SAM/BAM data

Commands

sambamba

Examples

View BAM file with filtering by mapping quality$ sambamba view -h -F 'mapping_quality >= 30' input.bam
Sort BAM file by coordinate$ sambamba sort -o sorted.bam input.bam
Count reads and calculate coverage statistics$ sambamba depth base -o coverage.txt input.bam