samtools

all

Tools for handling high-throughput sequencing (genomics) data. Used for reading/writing/editing/indexing/viewing of data in SAM/BAM/CRAM format.

Options (3)

-b, --bamboolean

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

Example: samtools view -S {{[-b|--bam]}} {{input.sam}} > {{output.bam}}

-h, --with-headerboolean

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

Example: {{other_command}} | samtools view {{[-h|--with-header]}} - chromosome:start-end

-o, --outputboolean

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

Example: samtools sort {{input}} {{[-o|--output]}} {{output.bam}}

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

samtools view -S [-b|--bam] 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|--with-header] - 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] 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