Annotate VCF/BCF Files
mehari annotates small variants (SNV/indel/MNV) with their predicted impact on gene transcripts and protein sequences, population frequencies (gnomAD, HelixMtDb), and ClinVar information.
mehari annotate seqvars \
--reference ref.fasta \
--transcripts transcript_db \
--frequencies gnomad_db \
--clinvar clinvar_db \
--input input.vcf --output output.bcf
Experimental Compound Variants
Evaluate the compound effect of multiple variants on the same transcript with our experimental compound variant analysis, choosing between strict, relaxed, or ignore phasing strategies.
mehari annotate seqvars \
--enable-compound-variants \
--phasing-strategy strict \
...
Build Databases from Arbitrary References
Build your own transcript databases directly from standard GFF3 annotations and FASTA reference sequences, or from Cdot JSON releases.
mehari db create txs \
--output custom_assembly.txs.bin.zst \
--transcript-sequences reference.fasta.gz \
--annotation reference_annotations.gff3.gz \
--assembly custom_assembly
Run as a REST server
Run mehari as a REST server with OpenAPI schema.
mehari server run \
--reference grch38=grch38.fasta \
--reference grch37=grch37.fasta \
--transcripts grch38.txs.bin.zst \
--transcripts grch37.txs.bin.zst \
--clinvar clinvar_db \
--frequencies gnomad_db
Python Bindings
Run variant annotation from within python.
from mehari import SeqvarsAnnotator
annotator = SeqvarsAnnotator(
transcript_db_paths=["path/to/txs.bin.zst"],
reference_path="path/to/reference.fa"
)
result1 = annotator.annotate("17:41197701:G:C")
result2 = annotator.annotate(chromosome="3", position=193332511, reference="G", alternative="T")
Interactive Variant Consequences
Have a look at our interactive consequences to find out about the Sequence Ontology terms used by mehari.
Authors and Contributors ⓘ
Groups, Institutes, Companies, and Organizations ⓘ
- Medizinische Genetik Mainz, Limbach Genetics
- @bihealth
- Cerebras