-
What is reported in github is not pseudo-log-likelihood:
https://github.com/ntranoslab/esm-variants/blob/main/esm_variants_utils.py#L90
Pseudo-likelihood requires masking each position one-by-one,…
-
Hi there,
I annotated a VCF of Clinvar variants using vcfanno and would like to create a database using vcf2db. However, there are no samples in the VCF. I tried adding a fake sample in the header …
-
This ticket aims to get a better handle on how oncogenicity and pathogenicity are related, and the constraints we should model around them with respect to variant origin, the disease object, and the s…
-
As part of the Variant Page effort, we have discussed to start developing the first two widgets (sample data has been shared on slack):
- [x] ClinVar
```
{
"alleleOrigins": [
"germli…
-
Initial notes on proposed scope and definition of these VA type, based on requirements and considerations documented [here](https://docs.google.com/document/d/1J4AqGDEqyK8KAzfiowgHYKJNvzHuwHSHgkN9dleL…
-
Integration of lists with information about chromosomal segments (including several genes e.g., ”chr22: 19,037,148 - 21,228,744”) for use in Scout in the same manner as we use gene lists. This is esse…
-
See also #154 - Variant Ranking / Prioritisation
Sarah raised an issue https://github.com/SACGF/variantgrid_com/issues/12
Background
In some cases it is not possible to reduce variants for investigat…
-
-
Suggestions by @vwirta :
- Type of causative vars (snv/SV) and the specific subcategory (frameshift, stop codon etc.)
- Compounds
- Clinvar classification of our causatives
- Population frequen…
-
Is it possible to use CHM13 as a reference for AnnotSV? Even if current annotations are just lifted from GRCh38 to CHM13 it would be very useful. Thank you!