With some newer VCF files, particularly those that have come from structural variant callers, the rownames of the resulting `VCF` objects (when the ID column is missing) can become problematic or excessively large. To give a concrete example, we have VCFs with insertions of dozens or hundreds of bases that lead to very long rownames. While human-readable rownames are useful in some cases, would it be possible to maintain uniqueness while enforcing some further constraints on the constructed rownames to keep them manageably short and printable?
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Yes, I can imagine that's the case. The pasting of CHROM:POS_REF/ALT was a reasonable solution when ALT was just a few bases. I'm open to other suggestions of how to handle this - what information would you like to see as the row names?
We do have the option to turn off rownames with readVcf(..., row.names=FALSE).