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  • Hkins552
    Member
    • Jun 2011
    • 18

    #1

    Phasing SNPs from sibs with no parents

    Hi All,
    I've recently called some SNPs from exome sequencing data on a family consisting of all siblings (no parent data available). I was wondering if there were any programs recommended by the community for phasing sibs without parents. I have .bcf and .vcf formats available and will need to work from there.
    Thanks,
    -Hkins
  • ulz_peter
    Senior Member
    • Feb 2010
    • 219

    #2
    I could recommend IBD2 (http://compbio.charite.de/index.php/ibd2.html) which calculates common haplotypes from a set of SNP calls (you need to first convert VCF files to a so-called ibs file format, but they provide a script).

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