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I'm exploring the new v4 data. I'm interested in the Pangolin scores. I notice the values are negative, when they should range from 0-1.
Please see this ticket for a similar SpliceAI Lookup issue:…
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Hej, I'm tinkering with VEP 111.0 in our wgs pipeline and ran into the following error when adding a VEP111 re-annotated case into scout.
```
Traceback (most recent call last): …
alkc updated
8 months ago
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The methods team has prepared a constraint hail table that is likely very close to the final schema.
This can be used to create a task for v4 constraint. The v2 constraint task can be referenced …
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I felt this might require its own issue. But related to #624.
There have been some breaking changes from VEP release 99 like gnomad column name changes IIRC.
How are these column names are handl…
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example: I would like to make a peppy.Project from a sample yaml file:
```
- sample_name: sample 1
file: path/to/file.tsv
- sample_name: sample 2
file: path/to/2.tsv
```
…
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## Describe the issue
We'd like to annotate a particular variant as an upstream_gene_variant w.r.t. a particular transcript. However, the variant impacts several other transcripts in their 5' UTRs, a…
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There's a `quality_metrics.allele_balance.bin_freq` somewhere that might be an array. It represents 5 percentile buckets of counts of samples with different allele balance scores. The last two buckets…
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gnomad tables have a field `lcr` somewhere, which is a boolean
output if true (not false/null):
```
{
"ancillaryResults": {
"low_complexity_region": true
}
}
```
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## Describe the issue
Hello everyone
I'm trying to annotate a vcf file on HG38 with many annotations
I'm using
`singularity exec -H /scratch4/references/vep_cache_singularity /scratch4/singular…
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## Symptom
E.g. http://myvariant.info/v1/variant/chrY:g.100005T%3EG?fields=dbsnp returns
```python
{
"_id": "chrY:g.100005T>G",
"_version": 1,
"dbsnp": {
...
"chrom": "X",
…