GA4GH htsget+Crypt4GH demo

Welcome to the first htsget-rs public instance with Crypt4GH support, hosted by GA4GH proper. Let’s begin with a simple curl command:

curl "https://htsget.ga4gh-demo.org/reads/service-info"

Which should yield the following JSON, please open a htsget spec browser tab on the side while you follow up:

{
  "id": "",
  "name": "GA4GH",
  "version": "0.1",
  "organization": {
    "name": "GA4GH",
    "url": "https://ga4gh.org/"
  },
  "type": {
    "group": "",
    "artifact": "",
    "version": ""
  },
  "htsget": {
    "datatype": "reads",
    "formats": [
      "BAM",
      "CRAM"
    ],
    "fieldsParametersEffective": false,
    "tagsParametersEffective": false
  },
  "contactUrl": "https://ga4gh.org/",
  "documentationUrl": "https://github.com/umccr/htsget-rs",
  "createdAt": "",
  "updatedAt": "",
  "environment": "dev"
}

Developers can now go and test the following endpoints with BAM and other formats (example files deployed from our htsget-рs data folder):

curl "https://htsget.ga4gh-demo.org/reads/htsgetlambdastack-bucket83908e77-0bbbuwy4lrax/bam/htsnexus_test_NA12878"

Check out the Crypt4GH encrypted BAM payload example file:

curl "https://htsget.ga4gh-demo.org/reads/htsgetlambdastack-bucket83908e77-0bbbuwy4lrax/c4gh/htsnexus_test_NA12878"

The payload can be decrypted with the test public/private keypair available on the official htsget-rs repo:

https://github.com/umccr/htsget-rs/tree/main/data/c4gh

Please read the included README.md keygen/encrypt/decrypt walkthrough for more details on how to work with those files.

CRAM files can be queried by specifying ?format=CRAM on the reads endpoint:

curl "https://htsget.ga4gh-demo.org/reads/htsgetlambdastack-bucket83908e77-0bbbuwy4lrax/cram/htsnexus_test_NA12878?format=CRAM"

And the equivalent Crypt4GH encrypted CRAM:

curl "https://htsget.ga4gh-demo.org/reads/htsgetlambdastack-bucket83908e77-0bbbuwy4lrax/c4gh/htsnexus_test_NA12878?format=CRAM"

Similar to the /reads endpoint, /variants is also supported for VCF and BCF files:

curl "https://htsget.ga4gh-demo.org/variants/service-info"

For example, to fetch the VCF example file, try:

curl "https://htsget.ga4gh-demo.org/variants/htsgetlambdastack-bucket83908e77-0bbbuwy4lrax/vcf/spec-v4.3"

Or, the same Crypt4GH encrypted VCF can be fetched with:

curl "https://htsget.ga4gh-demo.org/variants/htsgetlambdastack-bucket83908e77-0bbbuwy4lrax/c4gh/spec-v4.3"

BCF files can be obtained by specifying ?format=BCF on the variants endpoint. To get the example BCF:

curl "https://htsget.ga4gh-demo.org/variants/htsgetlambdastack-bucket83908e77-0bbbuwy4lrax/bcf/sample1-bcbio-cancer?format=BCF"

Or, the Crypt4GH encrypted BCF:

curl "https://htsget.ga4gh-demo.org/variants/htsgetlambdastack-bucket83908e77-0bbbuwy4lrax/c4gh/sample1-bcbio-cancer?format=BCF"

All the queries above that fetch data (excluding the service-info endpoint) support parameters which can restrict the regions returned.

For example, to query a specific reference name with start and end positions, try:

curl "https://htsget.ga4gh-demo.org/reads/htsgetlambdastack-bucket83908e77-0bbbuwy4lrax/bam/htsnexus_test_NA12878?referenceName=1&start=1000&end=2000"

Or, with the variants endpoint:

curl "https://htsget.ga4gh-demo.org/variants/htsgetlambdastack-bucket83908e77-0bbbuwy4lrax/vcf/spec-v4.3?referenceName=20&start=0&end=100"

This also works with Crypt4GH files, and it means that only specific regions that match the query will be returned:

curl "https://htsget.ga4gh-demo.org/reads/htsgetlambdastack-bucket83908e77-0bbbuwy4lrax/c4gh/htsnexus_test_NA12878?referenceName=1&start=1000&end=2000"

Or, with the Crypt4GH VCF file:

curl "https://htsget.ga4gh-demo.org/variants/htsgetlambdastack-bucket83908e77-0bbbuwy4lrax/c4gh/spec-v4.3?referenceName=20&start=0&end=100"

Our hope is that this public endpoint will facilitate much needed client implementations for Crypt4GH decryption, to name a few in no particular order:

• htsjdk
• IGV desktop
• IGV.js
• JBrowse2

So this is a call for library and client developers to test this htsget endpoint and report back!