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  • Where can I get GM19240 HapMap cell line variant calls as VCF or a BED file

    Hi:
    I am urgently looking for all the variant calls in either BED or VCF file for
    GM19240 and GM12878 HapMap cell lines.
    Could any one point me to sites where I can download all variant calls both SNPs and Indels for these two cell lines.

    thank you. Appreciate your help.

    -Adrian

  • #2
    I found this link where you can apparently download the entire latest hapmap build in vcf format (for sites and genotypes):

    ftp://ftp.broadinstitute.org/bundle/...9.sites.vcf.gz

    ftp://ftp.broadinstitute.org/bundle/....3.hg19.vcf.gz

    I did not download it but I suppose you can then filter out the information for the samples you are interested in.

    Cheers,
    Sophia

    PS.: In the table, the corresponding sample ID prefixes are NA- instead of GM- .
    Last edited by sdvie; 01-27-2012, 08:21 AM.

    Comment


    • #3
      Thank you Sophia.

      For some reason, I couldn't access the FTP site directly. However, the following helped to get access those files:

      ftp://[email protected]/1.2/hg19/

      Comment

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