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Update cheatsheets

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ivuorinen
2025-04-23 00:19:06 +00:00
parent 8ba6f7fc9e
commit 94c28849c9
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tldr/samtools
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@@ -11,15 +11,15 @@ source: https://github.com/tldr-pages/tldr.git
- Convert a SAM input file to BAM stream and save to file:
`samtools view -S -b {{input.sam}} > {{output.bam}}`
`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 - chromosome:start-end`
`{{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.bam}}`
`samtools sort {{input}} {{[-o|--output]}} {{output.bam}}`
- Index a sorted BAM file (creates `sorted_input.bam.bai`):