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samtools

Manipulate and analyze next-generation sequencing data files

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About

Tools for manipulating next-generation sequencing data

Commands

samtools

Examples

convert SAM file to BAM binary format$ samtools view -b input.sam -o output.bam
sort BAM file by genomic coordinates$ samtools sort input.bam -o sorted.bam
create index for BAM file for fast lookup$ samtools index sorted.bam
view mapping statistics and alignment summary$ samtools flagstat aligned.bam
extract reads mapped to specific region$ samtools view -b input.bam chr1:1000-2000 -o region.bam