Unsupported variant type CN0

[mshpak76]

When running snpEff on vcfs from a GWAS, I get a warning message:

java.lang.RuntimeException: Unsupported structural variant type '<CN0>'

snpEff seems to skip the line each time CN0 is encountered and continue to run. When I posed the query on biostars, someone directed me to a line of code in snpEff where e.g. CNV0 was the standard notation rather than CN0 etc.

I replaced all instances of CN with CNV in the input vcf using

sed 's/<CN\([0-9]*\)>/<CNV\1>/g'

However, now snpEff not only throws an error message when encountering CNV, but terminates the program:

java.lang.RuntimeException: Unimplemented method for variant type CNV

Other than changing CN0 to CNV0, is there some other formatting changes that need to be made?