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Mehari is a software package for annotating VCF files with variant effect/consequence.
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The program uses [hgvs-rs](https://crates.io/crates/hgvs) for projecting genomic variants to transcripts and proteins and thus has high prediction quality.
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Mehari offers predictions that aim to mirror VariantValidator, the gold standard for HGVS variant descriptions.
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Mehari offers HGVS predictions that aim to mirror VariantValidator, the gold standard for HGVS variant descriptions, and consequence predictions compatible with VEP.
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Further, it is written in the Rust programming language and can be used as a library for users' Rust software.
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## Supported Sequence Variant Frequency Databases
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Mehari can import public sequence variant frequency databases.
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The supported set slightly differs between import for GRCh37 and GRCh38.
To reduce compile times, we recommend using a pre-built version of `rocksdb`, either from the system package manager or e.g. via `conda`:
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```bash
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# Ubuntu
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sudo apt-get install librocksdb-dev
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# Conda
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conda install -c conda-forge rocksdb
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```
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In either case, either add
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```toml
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[env]
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ROCKSDB_LIB_DIR = "/usr/lib/"# in case of the system package manager, adjust the path accordingly for conda
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SNAPPY_LIB_DIR = "/usr/lib/"# same as above
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```
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to `.cargo/config.toml` or set the environment variables `ROCKSDB_LIB_DIR` and `SNAPPY_LIB_DIR` to the appropriate paths:
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```bash
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export ROCKSDB_LIB_DIR=/usr/lib/
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export SNAPPY_LIB_DIR=/usr/lib/
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```
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By default, the environment variables are defined in the `.cargo/config.toml` as described above, i.e. may need adjustments if not using the system package manager.
See [Getting Started](docs/getting_started.md) for more information on usage, and [Development Setup](docs/development.md) for more information on how to build mehari and its databases from scratch.
Copy file name to clipboardExpand all lines: docs/anno_seqvars.md
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- The predicted impact on gene transcripts and the corresponding protein sequence (in the case of coding genes).
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- Their frequency in the gnomAD exomes and genomes databases as well as the HelixMtDb database in the case of mitochondrial databases.
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- Variant information from ClinVar, if any
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## Command Line Invocation
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You can invoke Mehari like this to annotate a VCF file `IN.vcf`to an output file `OUT.vcf` using the built (or downloaded) database as `path/to/db`.
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You can invoke Mehari to annotate a VCF file `IN.vcf`creating an output file `OUT.vcf` using the built (or downloaded) databases – for example the transcript database – as follows:
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```text
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$ mehari annotate seqvars \
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--path-db path/to/db \
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--input-vcf IN.vcf \
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--output-vcf OUT.vcf
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--transcripts path/to/transcripts-db \
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--path-input-vcf IN.vcf \
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--path-output-vcf OUT.vcf
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```
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Note that the input and output files can optionally be gzip/bgzip compressed VCF files with suffixes (`.gz` or `.bgz`) or BCF files with suffix `.bcf`.
To reduce compile times, we recommend using a pre-built version of `rocksdb`, either from the system package manager or e.g. via `conda`:
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```bash
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# Ubuntu
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sudo apt-get install librocksdb-dev
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# Conda
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conda install -c conda-forge rocksdb
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```
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In either case, either add
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```toml
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[env]
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ROCKSDB_LIB_DIR = "/usr/lib/"# in case of the system package manager, adjust the path accordingly for conda
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SNAPPY_LIB_DIR = "/usr/lib/"# same as above
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```
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to `.cargo/config.toml` or set the environment variables `ROCKSDB_LIB_DIR` and `SNAPPY_LIB_DIR` to the appropriate paths:
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```bash
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export ROCKSDB_LIB_DIR=/usr/lib/
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export SNAPPY_LIB_DIR=/usr/lib/
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```
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By default, the environment variables are defined in the `.cargo/config.toml` as described above, i.e. may need adjustments if not using the system package manager.
Copy file name to clipboardExpand all lines: docs/index.md
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library.
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The latter serves as the basis for [VariantValidator.org](https://variantvalidator.org/) which is the gold standard for HGVS variant description generation and validation.
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- Mehari is written in the Rust programming language which allows it to work fast, with low memory consumption (as a C++ program would) and being memory safe at the same time (as a Java/Python/Perl program would).
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- As a Rust program, it can be embedded into the backend of the [VarFish](https://github.com/varfish-org/varfish-server) variant analysis platform.
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- It can be used as a rust library, as is the case for e.g. the backend of the [VarFish](https://github.com/varfish-org/varfish-server) variant analysis platform
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- Provides a REST API for sequence variant annotation (see `mehari server run --help`)
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## What's Next?
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Since Mehari is written in the Rust programming language, we host the documentation on `docs.rs` written as Rust online documentation.
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This has the advantage that the documentation is bundle with the program source code (and thus always up to date) and the latest documentation is always available at <https://docs.rs/mehari>.
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The drawback is that the formatting of this may not be as end-user friendly as it could be but you will manage.
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The drawback is that the formatting of this may not be as end-user friendly as it could be, but you will manage.
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?v=4&size=40){kind=avatar}
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