To annotate your vcf files, you need to run "new_run_snpeff.sh". You will need your vcf file, reference genome and snpeff.jar. SNPEFF is already an installed module by the HPCC Biocore. the reference genome is also a folder in snpeff. I am using GRCh38.v42 but you can switch to your desired genome
BEFORE RUNNING : Clone my repo and edit almost every line in new_run_snpeff.sh so that you specify your desired input, output folders, file locations, naming system and reference genome etc
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Links to Read "https://pcingola.github.io/SnpEff/se_running/" and "https://pcingola.github.io/SnpEff/se_human_genomes/"
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Scripts (Definitions coming soon)
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run_snp_eff.slurm -- slurm version of script above but can't get it to work because of memory issues with Java needing 8GB of free disk space and the SLURM cluster space limits
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check_var_types.sh -- checks what kinds of mutations are in the info column of vcf