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How to get nonvariant sites without the ref N sites.
I'm trying to get a vcf with the invariant sites i.e. select out ONLY the homozygous references sites in a multi-sample vcf (samples are either all 0/0 or a mix of 0/0 and ./.). I do not want the sites where the reference is N or all the sites are ./. (before filtering)
Is the only way to do this:
VariantFiltration with a filter QUAL > -1 (to remove the reference N sites)
selectVariants with --selectTypeToInclude NO_VARIATION