Is there an easy way to convert a VCF file to a XML file? I'm trying to find an easy way to produce a summary report by importing the XML file into a application like Microsoft Access.
Not directly. We have a tool called VariantsToTable that will produce a table of variants which you can then manipulate or convert fairly easily.
Thank you for the reply. I can't seem to find VariantsToTable. It's not in the list of downloadable software. Where do I find it?
Hi @davidrosewood. The VariantsToTable tool is already in the GATK toolkit you have downloaded. You just need to call VariantsToTable using the -T in the command line. Refer to Examples here: https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_VariantsToTable.html