Anders Jemt

Definitely interested! We validate our old germline pipeline by running GIAB samples as well as running a selection of our clinical samples with known pathogenic variants. We can also think...

Interesting will look into it

> Here are the emitted arguments. Maybe a typo for `gvcf_tbi`? indeed looks like a typo. Thanks for testing and reporting

Hi @vishramt7 and @asp8200, You're right that the conda part isn't that well tested as we've had issues getting some tools to run with conda, the SNV/INDEL caller deepvariant being...

At this moment, yes. It is stated in the prerequisites in the usage doc (https://github.com/nf-core/raredisease/blob/master/docs/usage.md#prerequisites) but we can add to the README as well. It would be nice to add...

If bgzip isn't available in he container, I would leave it as is. It needs to be bgzipped in order to be indexed and potentially merged back with the SNV...

One could look into adding it to the standard conda recipe of vcfanno to get it into the biocontainer, however it feels a little like we would hijack that conda...

Good idea, we're already using peddy from the same author to do ancestry, relatedness and sex check. He is suggesting switching to somalier as the more scalable solution. Will look...

Hi @egenomics, I've also noticed that `-resume` and I'm currently looking into that. Are these exome samples?

Hmm something seems to be off when combining the channels for going from a sample to case. From looking at the logs it looks like the samples aren't related in...