If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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 v220.127.116.11 | 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~