Exclude moltype cDNA from dbSNP137

myoglumyoglu Posts: 39Member

Hi!
Since dbSNP (for humans) has a lot of variants one could question if actually are real, especially those from cDNA (mRNA), how can I ignore all SNPs in dbSNP 137 with the moltype "cDNA"?

Im asking because a lot of these SNPs may actually be RNA editing artifacts, correct?

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  • myoglumyoglu Posts: 39Member

    Good, Ill try that one and post the solution when I figure it out.

  • myoglumyoglu Posts: 39Member

    I give up, I have to ask. I have opened the dbsnp_137.hg19.vcf file from your server and looked for anything that gives info about cDNA origin.. I cant find anything. I also tried to find other vcf from other places or something equal that had an info field about cDNA, no luck.

    Any help on this?

    I even emailed NCBI SNP admin, but with no answer.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,027Administrator, GATK Dev admin

    Ah, from your question I had assumed you had a VCF with that annotation; we don't have it in ours. If there's nothing in dbSNP to that effect, then I'm afraid you're out of luck, sorry.

    Geraldine Van der Auwera, PhD

  • myoglumyoglu Posts: 39Member

    Got it!

    UCSC browser:

    Go to tables -> group: variation and repeats, track: all SNPS (137) or the new 138..

    There’s a field for each snp called molType. Use the list of SNPs that have a molType of "genomic" and a class of "single".

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,027Administrator, GATK Dev admin

    Cool, thanks for reporting your findings.

    Geraldine Van der Auwera, PhD

  • myoglumyoglu Posts: 39Member

    No problem! Glad I can help. Maybe in the future dbSNP will be more valid.

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