Steps to install dependencies
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Miniconda installation Downlaod Miniconda python 3 version for linux bash Miniconda3-latest-Linux-x86_64.sh 1 a. Check for insatllation and config conda version conda list conda config --set auto_activate_base false
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Install snakemake using conda conda create -c conda-forge -c bioconda -n snakemake snakemake conda activate snakemake snakemake --help
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Install other tools dependencies a. Coverview b. CAVA c. ANNOVAR d. bedtools -- anaconda e. All variant callers ( use source code or binary installations -- do not use conda installation for lofreq) f. gatk 3.8 jar