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VCF does not handle "." in a FORMAT ID field (in the header) #328

Open LeeTL1220 opened 9 years ago

LeeTL1220 commented 9 years ago

##FORMAT=<ID=n.read.pos,Number=1,Type=Integer,Description="Number of unique read positions for the ALT">

The VCF spec does not state that this is ilegal. In a proposal to VCF 4.3, this is explicitly legal.

This will cause an error in pyVCF, which Oncotator uses.

Possible solution is to upgrade the version of pyVCF that Oncotator uses. Hopefully, this is all that is necessary.

LeeTL1220 commented 9 years ago

After examining code, it looks like this error will still exist.

LeeTL1220 commented 9 years ago

This may apply to INFO as well.