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VCF Annotator

The VCF Annotator tool provides utility for annotating VCF's with VRS Allele IDs.

How to use

Note:
The examples run from the root of the vrs-python directory and assumes that input.vcf.gz lives in the current directory

To see the help page:

python3 -m src.ga4gh.vrs.extras.vcf_annotation --help

Use local SeqRepo Data Proxy with default root directory

The tool uses a SeqRepo data proxy. By default, the local instance at /usr/local/share/seqrepo/latest is used.

Example of how to run:

python3 -m src.ga4gh.vrs.extras.vcf_annotation --vcf_in input.vcf.gz --vcf_out output.vcf.gz --vrs_pickle_out vrs_objects.pkl

--vcf_in specifies the path of the input VCF file to annotate. --vcf_out specifies the path of the output annotated VCF file. The --vrs_pickle_out specifies the path of the output pickle file containing VRS data (Both vcf_out and vrs_pickle_out are optional, but at least one must be provided).

Use local SeqRepo Data Proxy with different

You can change the root directory of SeqRepo by using seqrepo_root_dir.

To use the local SeqRepo data proxy with SeqRepo root directory at vrs-python/seqrepo/latest:

python3 -m src.ga4gh.vrs.extras.vcf_annotation --vcf_in input.vcf.gz --vcf_out output.vcf.gz --vrs_pickle_out vrs_objects.pkl --seqrepo_root_dir vrs-python/seqrepo/latest

Use the REST SeqRepo Data Proxy with default base url

You can change the data proxy type by using: --seqrepo_dp_type (options are local or rest).

To use the REST SeqRepo data proxy at default url: http://localhost:5000/seqrepo:

python3 -m src.ga4gh.vrs.extras.vcf_annotation --vcf_in input.vcf.gz --vcf_out output.vcf.gz --vrs_pickle_out vrs_objects.pkl --seqrepo_dp_type rest

Use the REST SeqRepo Data Proxy with different base url

You can change the SeqRepo REST base url by using: --seqrepo_base_url.

To use the REST SeqRepo data proxy, at custom url: http://custom.url:5000/seqrepo:

python3 -m src.ga4gh.vrs.extras.vcf_annotation --vcf_in input.vcf.gz --vcf_out output.vcf.gz --vrs_pickle_out vrs_objects.pkl --seqrepo_dp_type rest --seqrepo_base_url http://custom.url:5000/seqrepo

Other Options

--vrs_attribute

Will include VRS_Start, VRS_End, VRS_State fields in the INFO field.

--assembly [TEXT]

The assembly that the vcf_in data uses. [default: GRCh38]

--skip_ref

Skip VRS computation for REF alleles.

--require_validation

Require validation checks to pass in order to return a VRS object

--help

Show the options available