Select union of multiple-sample VCF
I have a multisample VCF with variants from 350 patient genomes. I'm trying to run a 'quick and dirty' Genomiser analysis to find high priority targets. In the absence of a pedigree, Genomiser is expecting a single VCF...and dies on the multiVCF. I'd like to take the union of all the variants across all the samples in this multisample VCF into a single new VCF that looks like one sample. Is there a good way to do this?
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Zcat2010 •
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GATK has "combine variants" tool: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantutils_CombineVariants.php