Where is the dbSNP information in oncotator result maf?

hexyhexy ChinaMember

I use oncotator v1.9 to annotate Tumor-Normal paired somatic variants in MAFLITE format. As the document described, there are 26 datasources:
_Oncotator v1.9.0.0 | 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~

Best Answer


  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @hexy, let's ask @LeeTL1220 to chime in here.

  • LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev ✭✭✭

    @hexy In MAF, the dbSNP results should always be in the 14th column dbSNP_RS... Are you saying that the column values are empty?

  • LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev ✭✭✭

    @hexy I've replicated a bug for rendering the DBSNP results. A fix should be coming ...

  • hexyhexy ChinaMember

    Thank you, @LeeTL1220, I have sovled it following the new version. And do you think it better to make the strict dependence more lenient, that is to change the dependencies from "==" to ">=" in setup.py file:
    _ install_requires=['bcbio-gff>=0.6.2', 'pyvcf >= 0.6.8', 'pysam >= **0.9.0', 'pandas>=0.18.0', 'biopython>=1.66', 'numpy>=1.11.0', 'cython>=0.24', 'shove>=0.6.6', 'sqlalchemy>=1.0.12', 'nose>=1.3.7', 'python-memcached>=1.57', 'natsort>=4.0.4', 'more-itertools>=2.2', 'enum34>=**1.1.2'],_

    because some the dependencies are too old to find the appropriate library, which makes the installaration difficult~
    Thanks again for helping me!

    Issue · Github
    by Sheila

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  • LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev ✭✭✭

    @hexy No problem.

    Actually, I have recently created the docker images using the static (i.e. ==) in the setup and virtualenv scripts and I had no trouble. In fact, years ago, we had the >= and that caused many issues, since interfaces or behavior would change and introduce bugs.

  • hexyhexy ChinaMember

    Hi, thanks for replying. I used ">=" for all dependencies, otherwise it will be not installed successfully and still now no bugs emerge, thanks again~

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