Nutty - a Sniffles companion app

Required programs (go)

Setup a conda environment for Nutty

conda create --name nutty python=3.10
conda install anaconda::go
conda activate nutty

Alternatively, you can use download go from https://go.dev/

How to run

Nutty can be used as without compilation using the following command:

go run main.go help

Or it can be compiled first

go run build

and then run

nutty help

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Examples

Run Nutty simple sample parser

# not compressed VCF
nutty sv --vcf sv.vcf

# compressed VCF
nutty sv --vcf sv.vcf.gz

# to get help with the parameters
nutty sv --help

Papers

In order to get reproducible results we included a paper subcomand that takes as input:

• Paper id
• VCF input
• Analysis flag and will output the output used for the analysis

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Note: Nutty is Sniffles friend in HPF