<p>Hi all,</p>

<p>I have a VCF file that was generated using HG18 and I want to convert it to VCF but that has HG19 data.</p>

<p>I am aware that there is the lift-over tool from UCSC but how do I convert a VCF file from HG18 to a VCF file to HG19, since it seems the lift-over tools produces a BED file instead.</p>

<p>Thanks in advance.</p>

You may use GATK "LiftoverVariants". It allows you to use VCF file as an input and outputs a VCF file corresponding to the new assembly. Link: https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_LiftoverVariants.php