Frequently Asked Questions

Data ingestion tools

Are Beacon v2 genomicVariations.variation.location.interval.{start,end} coordinates 0-based or 1-based?

They are 0-based

I have an error when attempting to use beacon vcf, what should I do?

  • In 9 out 10 cases, the error comes from BCFtools and is about the reference genome used. The reference genome is set up inside the parameters file and the possibilities are hg19, hg38 (both use chr before the number), and hs37 (does not use chr before the number). Be aware that BCFtools is very nit picky (with a reason) about the contigs, etc. not matching those in the fasta file. Please fix your VCF accordingly or modify config.yaml to provide the path to your reference genome.

  • On top of that, BCFtools may complain about the number of fields somewhere (e.g., at INFO) not being right.

INFO field IDREP only contains 1 field, expecting 2

You can try solving this issue manually or use bcftools annotate to get rid of the problematic fields, like this:

bcftools annotate -x INFO/IDREP input.vcf.gz | gzip > output.vcf.gz

Can I use SINGLE-SAMPLE and MULTI-SAMPLE VCFs?

Yes, you can use both. MongoDB allows for incremental loads so if you have single sample VCFs that's ok too (you don't need to merge them into a multisample VCF). The connection between sample and variants is performed at the datasets collection (and/or cohorts).

Can I use genomic VCF (gVCF)?

Yes, but first you will need to transform them to a VCF. There are quite a few sophisticated ways to do this (e.g., bcftools convert --gvcf2vcf --fasta ref.fa input.g.vcf). Here, we are not interested in having the whole genome positions, but rather the positions that contain ALT alleles. A "quick and dirty" solution to get those can be achieved with common Linux tools:

zcat input.g.vcf.gz | awk '$5 != "<NON_REF>"' | sed 's#,<NON_REF>##' | gzip > output.vcf.gz

Why are we re-annotating VCFs | Can I use my own annotations?

The underlying idea about annotating with the B2RI's data ingestion tools is to provide consistency/homogeneicity for the community. Technically speaking, to create genomicVariationsVcf.json.gz BFF, first we need to parse an annotated VCF. It's hard to create a parser that handles all the annotation alternatives from the community. On top of that, we need to make sure that the essential fields exist. That's why recommend annotating (or re-annotating if your VCFs already have annotations) VCFs with our tooling. Note that previous annotations in the VCF will be discarded.

Having said that, in ocassions researchers have internal annotations that can have a lot of value as well. For that reason, it is also possible to add alternative genomic variations by filling out the corresponding tab in the provided XLSX. Just make sure you fill out all the mandatory terms requested in the schema. The resulting file will be named genomicVariations.json. Both genomicVariations.json and genomicVariationsVcf.json.gz (see above paragraph) will end up loaded in the MongoDB collection genomicVariations. See more information in this tutorial.

Is there any alternative to the XLSX to introduce metadata/phenotypic data?

Yes, there is. You can use CSV or JSON directly as input. Please check the manual of the utility bff-validator.

bff-validator specification mismatches

By default, bff-validator will validate your data against the default schemas installed with your beacon2-ri-tools version. In this regard, it can happen that bff-validator gives you warnings on things that look OK elsewhere. An example of this could be warnings on objects matching more than one possibility in oneOf keywords. If this happens just use the flag --ignore-validation once you are ready to create your .json files.

Do you load all variations present in a VCF file?

Yes, we do not apply any filter such as using FILTER or QUAL fields (but we do store those values in case they need to be used a posteriori).

Do you have any recommendations in how to speed up the data ingestion process?

Usually, metadata/phenoclic data ingestion is fast as we'll be dealing with thousands of values (or dozens of thousands). Processing this should not take more than seconds/minutes.

VCF processing is what takes more time, in particular if you have WGS (e.g., you can have > 100M variants and thousands of samples). These are some recommendations:

  1. Split your VCF by chromosome.

    For this you can use community-tools:

    bcftools view input.vcf.gz --regions chr1
    

    or

    tabix -p vcf input.vcf.gz
    tabix input.vcf.gz chr1 | bgzip > chr1.vcf.gz
    

    or Linux tools (see more examples):

    zcat input.vcf.gz | awk '/^#/ || $1=="chr1"' | bgzip > chr1.vcf.gz
    
  2. Use parallel processing to submit the jobs.

Can I use parallel jobs to perform data ingestion into mongoDB?

Yes, yet this may slow down a bit the ingestion itself.

When performing incremental uploads, do I need to re-index MongoDB?

Nope. The indexes are created during the first load of key/values and updated automatically on every insert operation. Next attempts for re-indexing are simply discarded by MongoDB (i.e., the operation is idempotent).

Yes, but you need to request access and download it from the EGA. The VCF file contains WGS for 2,504 fake individuals (~20G). See more information here.

Beacon v2 API

Which tool do you recommend for making queries?

We recommend Curl.

Are aternative schemas supported?

A priori, Beacon v2 specification allows for alternative schema for the responses (e.g., Phenopackets). At this time (Apr-2022), this option is not supported by the Beacon v2 API.

Is the response data encrypted?

By default the API will start as http. The request/response can be encripted by adding the https protocol on top.

B2RI (General)

Is B2RI free?

Yes, it is open sourc and it is free. The data ingestion tools have GNU General Public License v3.0 and the API has Apache License v2.0.

The included CINECA_synthetic_cohort_EUROPE_UK1 dataset has CC-BY license.

Does it come with an UI (user interface)?

The simple answer is no. All tools are command-line based. But, we added a browser to visualize the contents of genomicVariations collection. This simple tool will (likely) cover many of the typical needs of a clinical geneticist/bioinformatician.

The long answer is that at CRG we're working on a full UI to work on top of the REST API.

Does B2RI include tools to create a Beacon Network?

Nope at this moment (Apr-2022). Currently, there is a Beacon scout team actively developing Beacon v2 Network API specification. See Beacon v1 Network API specification as a reference.

I am using a SQL-based database, can I still use your Reference Implementation?

The issue with having a SQL-based is that, if you want to be Beacon v2 response compliant you will need to convert your tables-based data to the JSON Schema of the Beacon v2 Models. Intrepid implementers are able to do this transformation (likely) at the API level. However, a much simpler alternative (and actually the one we've seen the most in healthcare systems) is that people perform a dump (data export) of the subset of data they want to share and then use B2RI tools to convert this tabular data to Beacon v2 format and use the included REST API. So yes, if you follow this path you will be still using our Reference Implementation.

Should I update to the latest version?

Yep. We recommend checking our Github repositories (beacon2-ri-tools and beacon2-ri-api) and downloading the latest version. If the version it's in GitHub is because it passed our test and it's ready to be used. In principle, a simple git pull will do the update for both containerized and non-containerized versions. Now, the version number matches that of the Beacon v2 specification. When the latter changes, B2RI version will change as well.

Can I contribute to the GitHub repositories?

Please contact the authors.

How do I cite B2RI?

Citation

Rueda, M, Ariosa R. "Beacon v2 Reference Implementation: a toolkit to enable federated sharing of genomic and phenotypic data". Bioinformatics, btac568, DOI.