How to run SNPEff jar for a batch of VCF files using GNU parallel tool?
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3.4 years ago
oxfordsoccer ▴ 10

How to run SNPEff jar for a batch of VCF files (300 items) using GNU parallel tool? Need a code example. Found only one example somehow similar to my question https://stackoverflow.com/questions/28072857/s-gnu-parallel-execution-of-commands-from-file-few-at-a-time. Thx.

snpeff gnu parallel software variant calling bash • 1.4k views
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I think you need to use:

GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. The typical input is a list of files, a list of hosts, a list of users, a list of URLs, or a list of tables. A job can also be a command that reads from a pipe. GNU parallel can then split the input and pipe it into
commands in parallel.

Nice tutorial can be found:

https://davetang.org/muse/2013/11/18/using-gnu-parallel/

https://www.codeword.xyz/2015/09/02/three-ways-to-script-processes-in-parallel/

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If you add an example of how you do it without GNU Parallel, then you may have more luck getting a usable answer.

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