phenopackets_v1_to_v2.md

Converting Phenopackets from V1 to V2 using bentoctl

Phenopackets JSON documents can be converted from V1 to V2 using bentoctl and Phenopacket-tools as its backend.

For the bentoctl convert-pheno command to work, you need to:

1. Download a Phenopacket-tools release.
2. Unzip its content and place the .jar file somwhere safe.
3. Specify the .jar path in local.env with the PHENOTOOL_JAR_PATH variable

You can then convert a file with:

bentoctl convert-pheno <source> <target>

If the target argument is not provided, bentoctl will append "_pheno_v2" to the source file's name and save it in its parent directory.