I need to convert phased data (map and haplotype file) from the Hapmap Phase II data to vcf files.
Are you familiar with any software that makes the conversion?
You may want to take a look at the GATK VariantsToVCF tool: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_VariantsToVCF.html
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