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Old 08-18-2011, 12:02 PM   #1
Hkins552
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Location: Baltimore MD

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Question 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
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Old 08-18-2011, 11:21 PM   #2
ulz_peter
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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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