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About the GATK resource bundle

HyunminHyunmin Seoul, KoreaMember Posts: 14
edited January 2014 in Ask the GATK team

Dear GATK team,

When I annotate the dbsnp id to my vcf, I used the dbsnp 137 vcf file in resource bundle.
but, it has some entry in original dbsnp137.
This mean it has different entry in dbsnp137 (from UCSC). One example is dbsnp id in MT chromosome.
so, I can't get fully annotated dbsnp, when I using the dbsnp 137 in gatk resource bundle.

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin

    I'm sorry, I don't understand your question. Can you maybe provide an example of what the problem is?

    Geraldine Van der Auwera, PhD

  • HyunminHyunmin Seoul, KoreaMember Posts: 14
    edited January 2014

    @Geraldine_VdAuwera said:
    I'm sorry, I don't understand your question. Can you maybe provide an example of what the problem is?

    Sorry for my eng. I don't have an example now. (about a month ago..).
    I changed my question.
    Is it different GATK Bundle dbsnp137 (dbsnp_137.hg19.vcf) with UCSC dbsnp137 (snp137.txt.gz)?

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