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dbsnp file in unified genotyper

HomaHoma Posts: 7Member

Hi,

I am using unified genotyper utility of GATK. I don't exactly know how I should make the dbsnp file necessary. I thank you very much for any help.

Regards, Homa

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,089Administrator, GATK Developer admin

    I'm sorry, I don't understand your question. The dbsnp file is not required by the UnifiedGenotyper but it can be used if you want. Are you trying to use it and it's not working? Or is your problem something else?

    Geraldine Van der Auwera, PhD

  • namsyvonamsyvo Posts: 1Member
    edited April 3

    I want to make sure about one problem related to this topic. As I understand from the GATK-UGT document, dbSNP files are not used to verify called SNPs in any way while performing SNP calling with GATK-UGT, is that correct?

    --dbsnp / -D dbSNP file rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate. dbSNP is not used in any way for the calculations themselves. --dbsnp binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3

    Nam.

    Post edited by namsyvo on
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,089Administrator, GATK Developer admin

    Hi Nam, they are used only for annotating the rsID if a variant has been reported previously. They are not used in any way to decide whether variants should be emitted.

    Geraldine Van der Auwera, PhD

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