Octopus joint genotyping config

[DiDeoxy]

Hello, I am trying to do joint genotyping with gvcfs produced by the Octopus variant caller. There isn't a preset (yet?) so I am trying to roll my own but glnexus wont read what I have written.

[error] Failed to load unifier/genotyper configuration: IOError: loading configuration YAML file (octopus.yml)

This is a rather cryptic error message so I was hoping you could help.

Here is my config file:

octopus.zip

I am assuming I don't need to add the GT or DP format fields.

Cheers,

Max H.

[DiDeoxy]

I fixed the error for PS where I had int instead of string, still not working

[mlin]

The only thing that jumps out as me is all the keys in each liftover_fields item should be at the same indent level. I'd like to help, are there any public corpi of octopus gvcf suitable for unit testing purposes?

[DiDeoxy]

barley_octopus_gvcfs.zip

Here are some I've made from barley public data. I have more if needed.

[DiDeoxy]

you were right about the formatting, thanks!

[xiekunwhy]

GLnexus support Octopus gvcf now?