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Running SnpEff on MacOS using Anaconda #256

Closed Suuusj closed 3 years ago

Suuusj commented 3 years ago

Hi all,

I am kinda new to this field, so my apologies in advance.

I am trying to run SnpEff on my Mac using Anaconda. I think I managed to install the package (conda install -c bioconda snpeff), now I try to run the tool which is where I am stuck.

What would be the command line code that should be used to run the tool, and which input does it require? Only a VCF file?

I expect it to be something like; snpeff - input.vcf -output.vcf ?

Thanks in advance for helping out

Suzanne

pcingola commented 3 years ago

There are plenty of examples and guidance in the documentation: https://pcingola.github.io/SnpEff/ss_introduction/

Also there is a specific "examples" section in SnpEff's website: https://pcingola.github.io/SnpEff/examples/