Closed brmyers closed 5 years ago
@brmyers , Good point about the ID delimiter.
The use of the GQ field for genotype information was intentional. Admittedly, the specification indicates this should be a phred-scaled quality score, which is not true of the array quality scores; however, there is some benefit to re-using the "standard" field for quality information.
Created pull request at https://github.com/Illumina/GTCtoVCF/pull/29
Fair point about reusing GQ @KelleyRyanM, but it's worth mentioning that htsjdk (not sure about other VCF libraries) changes the GQ/Format header to an integer and rounds the values in the records to zero or one.
Appreciate the quick reply.
Thanks for the software. While using it, I discovered two items that are not following the VCF specification. https://samtools.github.io/hts-specs/VCFv4.2.pdf
I'm doing some post-processing as a workaround, but figured I'd mention my findings.
Best, Ben