functional annotation

Hello,
I'm trying to do functional annotation on variants called by HaplotypeCaller from P. vivax whole genome sequences using snpeff version 3.6b, but I get the error "WARNING: Unkown IUB code for SNP '*'Error while processing VCF entry (line 3078)." I see in the forums that later snpeff versions are no longer supported, should I use a different program for functional annotation?
Thanks!

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