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Once sequence annotations is implemented, a search by feature ID for variant annotations should be added back in.
https://github.com/ga4gh/schemas/issues/577
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Variant annotation supports searching by referenceName and referenceId. Currently, only search by referenceName is supported.
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The README.md mentions the script `var-pt-map.py`, but I can't find this script in the repository. I'm very interested in it, if you're able to share it alongside the Jupyter notebooks you've already …
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Hi,
I'm trying to annotate a VCF with only 248 variants using the gnomad genomes VCF as annotation and it takes about 2 hours to run. Both the input VCF and the annotation VCF are indexed with tab…
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**Describe the bug**
The Variant DEL-grch37-5-150175225-150181898 overlaps 3'utr instead of coding sequence. This should be clearly reflected in the consequence annotation.
**To Reproduce**
TBD
…
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Hello,
I noticed that in the case of annotated multiallelic VCF where annotation for each alternative is stored in the INFO field, `variant.INFO.get("annotation")` would only pick the first occurre…
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Hi,
First of all, we want to thank you for this wonderful application. It has streamlined our variant annotation workflow tremendously.
We submitted the HG19 chr16-11349332-CC-TT variant to Ope…
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I gather there's an idea for material prefixes of some sort,
but could we add some common cases to the label list to enable annotating these sooner rather than later.. and map them back to the materi…
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Hi,
I tried to run your test_data, but I got this error:
```
########################################################
###### SV-HotSpot v1.0.0 ######
####################…
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Working in branch **partition_by_contig**
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Then add contig to every query, this would presumably speed up eg gene and variant queries (as we'd have much smaller table to scan)
Remember to…