tldr/pages/common/samtools.md

# samtools

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

- 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}}`