Comments (1)
kaichop
commented on July 16, 2024
This is a known problem. The reason is that this particular mutation has no meaning based on VCF format specification (there is no alternative allele, and the GT field is listed as 0/0).
1 9407759 . AC . 86.73 . AN=2;DP=34;MQ=60.0 GT:AD:DP 0/0:34:34
I had previously updated convert2nnovar.pl to handle this particular situation (essentially treating the ALT as "0", so at least gene-based and region-based annotation can work) but never updated the package itself. I will include this in the latest package to be released soon.
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