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  • memento
    Member
    • Nov 2010
    • 49
    #1

    dbsnp135 vcf on an alignment with hg19

    i was wondering if there is any vcf file (dnsnp135) prepared to be compatible with hg19 ?

    ftp://ftp.ncbi.nih.gov/snp/organisms.../00-All.vcf.gz

    Is this one usable with hg19 ?

    anyone posted liftover'd version of dbsnp135 for a hg19 ?
    Last edited by memento; 02-03-2012, 10:34 AM.
    Tags: None
  • Heisman
    Senior Member
    • Dec 2010
    • 534
    #2
    when I looked at dbSNP135 about two months ago, there were a lot of errors. Not sure if they've been fixed. Just throwing that out there to be cautious.

    Comment

    • memento
      Member
      • Nov 2010
      • 49
      #3
      db132 is currently the one supported by GATK. Its good enough ?

      Comment

      • Heisman
        Senior Member
        • Dec 2010
        • 534
        #4
        I have not read anything to indicate that it isn't.

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