mehari

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fix: allow multiple references in mehari server run

1

Support multiple references in `mehari server run`, e.g. ``` mehari server run \ --transcripts GRCh38-ensembl.bin.zst \ --transcripts GRCh37-ensembl.bin.zst \ --reference GCF_000001405.40_GRCh38.p14_genomic.fna \ --reference GCF_000001405.25_GRCh37.p13_genomic.fna ``` Note that this relies on...

tedil

Usage question, mehari server run and multiple references

2

Hi, thank you for mehari. It's impressive how fast it works. Thank you for sharing it with the community. I have a question about a server usage. ``` mehari server...

pstawinski

feat: Plugin system (#426)

2

This draft PR adds a plugin system based on [extism](https://extism.org/) (#426). To that end, the project is converted to a workspace with (currently) three members: `mehari`, `mehari-plugins` and `mehari-plugin-vep-nmd`. -...

tedil

**Is your feature request related to a problem? Please describe.** In a case/pedigree with multiple samples some variants may not have usable data from all samples (either due to missing...

Nicolai-vKuegelgen

**Is your feature request related to a problem? Please describe.** The `mehari annotate seqvars` command with the `--path-output-tsv` option, will *always* select a single transcript even with the implied default...

Nicolai-vKuegelgen

Define transcript preference

1

**Is your feature request related to a problem? Please describe.** In the case that both ENSEMBL and RefSeq sources have MANE transcripts, there is no rule which one to prefer....

holtgrewe

Genome builds have no unified format

4

**Describe the bug** Currently genome builds have different "names"/"labels" in different APIs. For example: https://reev.cubi.bihealth.org/internal/proxy/mehari/genes/txs?hgncId=HGNC:4806&genomeBuild=GENOME_BUILD_GRCH37&pageSize=1000 https://reev.cubi.bihealth.org/internal/proxy/mehari/seqvars/csq?genome_release=grch37&chromosome=6&position=24302274&reference=T&alternative=C **To Reproduce** N/A **Expected behavior** There should be one standard for genome builds across...

gromdimon

unannotated MT variants for RefSeq

5

**Describe the bug** We noticed that there are MT variants that have been annotated with Ensembl information but the RefSeq information is empty. We need to double check why this...

stolpeo

Implement multiallelic variants/variant normalization

2

**Is your feature request related to a problem? Please describe.** Currently, mehari does not support multi-allelic sites. This is a big limitation and requires `bcftools norm -m -any --force`. **Describe...

holtgrewe

Compare mehari annotation with VEP annotation

3

- build mehari transcript DB (ensembl): - download cdot for ensembl and grch37 / grch38 - download ensembl FASTA for transcripts - create / fill seqrepo with ENSEMBL FASTAs -...

tedil