Closed geocarvalho closed 2 years ago
Hello @geocarvalho , If you notice carefully, you will find that all these variants are composed by Nirvana ("isRecomposedVariant": true). They do not come from the variant caller. For these variants, we cannot provide "variantFrequencies", "fisherStrandBias", "mappingQuality", and "alleleDepths" annotations. We decided against attempting to aggregate these values from the constituent SNVs since it was not clear how it could be done uncontroversially.
Best Rajat
Hello, thanks to make this great project available as open source. I was creating a table for some variants annotated with Nirvana and I found some cases (21 MNVs from 300k variants) that the variant doesn't have "variantFrequencies", "fisherStrandBias", "mappingQuality", and "alleleDepths" annotations, but I can see the "AD" and "AF" information inside the VCF for the SNVs separately. Three examples:
Would be great to have all the annotations. Is it somehow expected?
Nirvana 3.16.1 Cache version: 27, Supplementary annotation version: 63, Reference version: 7
usingGRCh38
Best, George.