gcp-variant-transforms
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Published
20 hours ago •
googlegenomics
googlegenomics
Better communicate reference sequence mismatch, when running variant annotation.
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Currently we have --check_ref enabled when running VEP. This generates a list of reference mismatches if the VEP cache used is for a different reference sequence than the one used to create the input VCF.
This information should be communicated clearly to the user, instead of them checking the output files and fishing for such warning messages.
The mismatch variants are also dropped and this needs to be communicated to the user. Also it would be nice to detect the mismatch issue and fail or warn early.