samtools:tldr:0f0c3

samtools: Split input file according to read groups.

samtools

$ samtools split ${merged_input}

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The command samtools split ${merged_input} is using the "samtools" tool to split a merged SAM or BAM file into individual read files.

Here is a breakdown of the command and its components:

samtools: It is a widely-used command-line program for working with SAM (Sequence Alignment/Map) and BAM (Binary Alignment/Map) files. It provides various functions for manipulating and analyzing these files.
split: It is one of the functions provided by samtools. It is used to split a merged SAM or BAM file into separate read files based on their read groups or other criteria.
${merged_input}: It is the input file or variable containing the path to the merged SAM or BAM file that needs to be split. The ${...} syntax is commonly used to refer to a variable in bash or other scripting languages. It means that the actual value of the variable should be substituted in its place.

When this command is executed with the appropriate input file provided, samtools will split the merged file into several individual read files based on their read groups or other specified criteria. This can be useful for downstream analysis that requires separate files for each read or read group.

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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