SnpSift GeneSets - SnpEff & SnpSift
Author: Pablo Cingolani
Description: SnpEff and SnpSift

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# SnpSift GeneSets

Annotating GeneSets, such as Gene Ontology (GO), KEGG, Reactome, etc.; can be quite useful to find significant variants.

Gene set annotations can be added to a SnpEff annotated file using `SnpSift geneSets` command. The VCF file must be annotated using `SnpEff` before performing Gene Sets annotations. This is because we must know which gene the variant affects).

Info

You can download MSigDb from Broad Institute

Usage example:

    $ java -jar SnpSift.jar geneSets -v db/msigDb/msigdb.v3.1.symbols.gmt test.ann.vcf > test.eff.geneSets.vcf
    00:00:00.000    Reading MSigDb from file: 'db/msigDb/msigdb.v3.1.symbols.gmt'
    00:00:01.168    Done. Total:
            8513 gene sets
            31847 genes
    00:00:01.168    Annotating variants from: 'test.ann.vcf'
    00:00:01.298    Done.
    # Summary
    #       gene_set    gene_set_size   variants
    #       ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN   940 8
    #       CHR1P36 504 281
    #       KEGG_OLFACTORY_TRANSDUCTION 389 8
    #       REACTOME_GPCR_DOWNSTREAM_SIGNALING  805 8
    #       REACTOME_OLFACTORY_SIGNALING_PATHWAY    328 8
    ...
    #       REACTOME_SIGNALING_BY_GPCR  920 8

    $ cat test.eff.geneSets.vcf
    ## INFO=<ID=MSigDb,Number=.,Type=String,Description="Gene set from MSigDB database (GSEA)">
    1   69849   .   G   A   454.73  PASS    AC=33;EFF=STOP_GAINED(HIGH|NONSENSE|tgG/tgA|W253*|305|OR4F5|protein_coding|CODING|ENST00000335137|1|1);MSigDb=ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN,CHR1P36,KEGG_OLFACTORY_TRANSDUCTION,REACTOME_GPCR_DOWNSTREAM_SIGNALING,REACTOME_OLFACTORY_SIGNALING_PATHWAY,REACTOME_SIGNALING_BY_GPCR