samtools

Tools for handling high-throughput sequencing (genomics) data.

Used for reading/writing/editing/indexing/viewing of data in SAM/BAM/CRAM format.

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• Convert a SAM input file to BAM stream and save to file:

samtools view -S -b {input.sam} > {output.bam}

• Take input from stdin (-) and print the SAM header and any reads overlapping a specific region to stdout:

{other_command} | samtools view -h - chromosome:start-end

• Sort file and save to BAM (the output format is automatically determined from the output file's extension):

samtools sort {input} -o {output.bam}

• Index a sorted BAM file (creates {sorted_input.bam.bai}):

samtools index {sorted_input.bam}

• Print alignment statistics about a file:

samtools flagstat {sorted_input}

• Count alignments to each index (chromosome / contig):

samtools idxstats {sorted_indexed_input}

• Merge multiple files:

samtools merge {output} {input1 input2 …}

• Split input file according to read groups:

samtools split {merged_input}

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