1.0. Sort and index your BAM files using script and samtools

If you have to do repeated operation with your multiple files in a command line you better write a script. Traditionally shell scripts are used. But if you do not know shell you can write it in python or R where you make use of a "system" function to communicate with the terminal. Here is an example of sorting and indexing multiple bam files in zsh, python and R in macOS environment. #shell #zsh #python #r #bam #samtools #sort #index