VariantAnnotation_1.16.4 in R version 3.2.0 with Bioconductor 3.2 is printing maformatad vcf files that cannot be read by e.g. GATK.

variants with alt allels like for instance

*,G

are turned into

,G

Furthermore after correcting. The vcf malformated so that The allele with index 2 is not defined in the REF/ALT columns in the record. Which I have no idea what it means or . 

Thanks,

The current release version of VariantAnnotation is 1.18.6 and devel is 1.19.9. We don't support (i.e., make changes to the code base) older versions. Please update R to 3.3 and Bioconductor to 3.3 (release) or 3.4 (devel) and let me know if the problem persists.

Valerie