mirror of
https://github.com/tldr-pages/tldr.git
synced 2025-04-24 01:22:10 +02:00
a5fe31bc47
Co-authored-by: bl-ue <54780737+bl-ue@users.noreply.github.com> Co-authored-by: Starbeamrainbowlabs <sbrl@starbeamrainbowlabs.com>
36 lines
1 KiB
Markdown
36 lines
1 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}}`
|