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  • 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.

  • #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.

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    • #3
      db132 is currently the one supported by GATK. Its good enough ?

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      • #4
        I have not read anything to indicate that it isn't.

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