Add CoLoRSdb and gnomAD keys

[fellen31]

Would it be a good idea to add allele frequencies from Consortium of Long Read Sequencing Database (CoLoRSdb), preferably as colorsdb_af?

Could I also get gnomad_af and gnomad_popmax_af added as gnomAD keys? 😃

[dnil]

Yes, let's add CoLoRSdb. Is the lower case string its standard key?

And what's with the gnomAD lower case INFO keys? 😆 Is this from a new VEP version, or are you freestyling a little? Could we expect to see them from other pipes as well?

[dnil]

Don't get me wrong, it does make sense; I'm pretty annoyed with things like gnomADg_AF_POPMAX, not to mention happy not to have to add a case sensitive CoLoRSdb. 😄

[fellen31]

The lowercase gnomAD keys come from using echtvar instead of VEP to add the frequencies. They supply a pre-encoded gnomad database at a handy size (~7 GB), where the keys are encoded as lowercase.

The CoLoRSdb VCF key is AF so I set it to colorsdb_af.

[dnil]

Supporting Brents stuff out of the box sounds nice, and following the pattern for CoLoRSdb seems like a plan. It will be the first set of AFs that don't end in capital AF. 😆

[dnil]

Do we have example files somewhere?

[fellen31]

Do we have example files somewhere?

/home/proj/development/rare-disease/felix/scout_test/filtered.vcf.gz

This one has gnomad_popmax_af and colorsdb_af but no gnomad_af. If you want to have all I can update it.

[northwestwitch]

This one has gnomad_popmax_af and colorsdb_af but no gnomad_af. If you want to have all I can update it.

Hi @fellen31 I'm working on this issue now. Would be nice to have an example with all 3, also super small would be fine, so I can copy one variant from it to include in the automatic tests of scout. But we can also add the test for gnomad_af later, so no rush!

[fellen31]

Hi, I've updated the same file to include all three!

[northwestwitch]

Hi, I've updated the same file to include all three!

Nice, thanks!