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Where is the dbSNP information in oncotator result maf?
I use oncotator v1.9 to annotate Tumor-Normal paired somatic variants in MAFLITE format. As the document described, there are 26 datasources:
_Oncotator v126.96.36.199 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ExAC 0.3.1 | dbSNP build 142 | COSMIC v76 | 1000gp3 20130502 | dbNSFP v2.4 | ClinVar 12.03.20 | ORegAnno UCSC Track | CCLE_By_GP 09292010 | UniProt_AA 2014_12 | Ensembl ICGC MUCOPA | COSMIC_FusionGenes v76 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue v76 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | TCGAScape 110405 | MutSig Published Results 20110905 _
I got a 348 columns maf for each sample, but information about dbSNP is empty, such as dbSNP_RS(column 14) and dbSNP_Val_Status(column15). The dbSNP populaiton informaiton cannot find, what I mean is something like "1000gp3_EAS_AF". What should I filter the dbSNP database?
How to annotate germline variants? Could I use oncotator?
Thx andvance if anyone help me out~