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samtools:tldr:8b455

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

samtools

$ samtools sort ${input} -o ${output-bam}

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This command is using the software tool "samtools" to sort a SAM or BAM file.

Here is a breakdown of the command:

${input}: The input variable refers to the input SAM or BAM file that you want to sort. This variable is being passed to the samtools sort command.
samtools sort: This is the command to sort a SAM or BAM file using samtools.
-o: This option specifies the output file name or the path to where the sorted BAM file should be saved.
${output-bam}: The output-bam variable holds the name of the sorted BAM file. This variable is being passed as the value for the -o option.

Overall, this command takes an input SAM or BAM file, sorts it using samtools, and then outputs the sorted BAM file to the specified location.

This explanation was created by an AI. In most cases those are correct. But please always be careful and never run a command you are not sure if it is safe.

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