Changes between Version 2 and Version 3 of SOPs/genome_regions_annotations


Ignore:
Timestamp:
10/22/13 10:13:36 (11 years ago)
Author:
gbell
Comment:

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  • SOPs/genome_regions_annotations

    v2 v3  
    119119
    120120On Whitehead servers, pre-installed genomes (with annotations) can be chosen from the directory names in /usr/local/share/snpEff/data
     121
     122Creating a novel database for snpEff
     123  * Make a copy of the snpEff config file containing the path to your new database (ex: ~/snpEff/data/myGenome.v1)
     124  * In that directory (ex: data/myGenome.v1) put the genome (called ''sequences.fa'') and a GTF file describing the genes (called ''genes.gtf'').
     125  * Go to that directory and run
     126      * java -jar /usr/local/share/snpEff/snpEff.jar build -gtf22 -v myGenome.v1
     127  * Now there should be a new file: data/myGenome.v1/snpEffectPredictor.bin