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