tldr/pages/common/samtools.md

37 lines
1.0 KiB
Markdown

# 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}}`